Ok, a few comments.
First of all, you're getting focused senses awfully late. You will feel this, in the form of debt. I really recommend getting toggles as soon as you can. You get 2 passives before your 2nd toggle. Change this. If you choose between a toggle and a passive, ALWAYS choose the toggle.
Second, I've looked into it a bit, 3 end reduxes on your toggles is overkill. The third slot won't do anything usefull anymore. I say drop one in each toggle, and get 2 max. (except focused accuracy, getting 3 is prolly a good idea there)
Your current attack slotting is 3 dmg - 2 acc - 1 end. This is a very decent slotting, but I did fine with 3 dam - 1 acc - 1 end - 1 recharge. Keeps the attack chain much more fluent.
Also, I think thunder kick is a poor power. IMO, crippling axe kick (CAK) is better. Yes, the animation takes a while, but its your third most damaging attack and most importantly, it immobilizes and slows stuff on top of the good damage. This can be VERY usefull! (especially in PvP)
And finally, personally I think the fighting pool is of limited use. Tough only grants defense against smashing/lethal, and weave gives just a tiny bit of defense. (less then your passives do IIRC)
My advice: drop fighting pool and get medicine (aid other - aid self). This way you free up a power slot, and aid self is AWESOME for a /SR. Slot it 3 heals and at least 1 reduce interrupt (I have yet to experiment with 2 or even 3 interrupt reductions) and whenever you get into trouble, hit aid self. Your defense means you get hit less, and this means you don't get interrupted all that often. Slotted with 3 heals, this power heals more then a lvl 2 healing insp!!! (more then a third of your health)
Sorry for the huge post. I love MA/SR 
I can recommend Cobra Strike, it's amazingly useful for taking an opponent out of the fight for a while. Slotted with a couple of Disorient enhances it'll last long enough to dispatch two guys before your Cobra Struck guy comes round.
As ToughGuy says the Fighting pool isn't that great for an SR Scrapper, besides which you can get an epic pool instead between 41 and 50. Most Scrappers seem to go for Body Mastery for the Focused Accuracy (very nice for spotting Stalkers), but Weapon Mastery gives you Caltrops (always good to have) and Shuriken (surprisingly underrated IMO). Darkness Mastery has some nice control too with a hold and an AOE immobilise, as well as a couple of blast type attacks.
After you take Stamina, take hasten as well. You can fire off attack after attack and barely make a dent in your endurance.
-Take Focused Senses and Practiced Brawler earlier, they're pretty much more important than everything you've put before them.
-Fighting pool isn't my bag, tough is arguable but weave is pretty much pointless.
-While you may consider respeccing out thunder kick for CAK eventually, it will seve you well for now since you are unlikely to take many attacks after thunder, storm and crane until the mid twenties.
Because I'm too lazy to give real advice I'm just going to post my build below in case it helps with slotting.
Exported from version 1.5C of CoH Planner
http://joechott.com/coh
Archetype: Scrapper
Primary Powers - Ranged : Martial Arts
Secondary Powers - Support : Super Reflexes
01 : Focused Fighting defbuf(01) defbuf(3) defbuf(3) endred(5)
01 : Storm Kick dam(01) dam(5) dam(7) acc(7) acc(9) endred(43)
02 : Focused Senses defbuf(02) defbuf(9) defbuf(11) endred(11)
04 : Cobra Strike disdur(04) disdur(13) disdur(13) acc(15) acc(15) endred(43)
06 : Focus Chi recred(06) recred(17) recred(17)
08 : Crane Kick dam(08) dam(19) dam(19) acc(21) acc(21) endred(43)
10 : Hasten recred(10) recred(23) recred(23)
12 : Practiced Brawler recred(12) recred(25) recred(46)
14 : Super Speed runspd(14)
16 : Hurdle jmp(16)
18 : Health hel(18) hel(42) hel(46)
20 : Stamina endrec(20) endrec(25) endrec(27)
22 : Quickness runspd(22)
24 : Aid Other hel(24) hel(48)
26 : Dragons Tail dam(26) dam(27) dam(29) acc(29) endred(37) recred(45)
28 : Crippling Axe Kick dam(28) dam(31) dam(31) acc(31) acc(33)
30 : Aid Self hel(30) hel(33) hel(33) inttim(34) inttim(46) recred(50)
32 : Eagles Claw dam(32) dam(34) dam(34) acc(36) acc(36) recred(40)
35 : Evasion defbuf(35) defbuf(36) defbuf(37) endred(37)
38 : Elude defbuf(38) defbuf(39) defbuf(39) recred(39) recred(40) recred(40)
41 : Conserve Power recred(41) recred(42) recred(42)
44 : Agile defbuf(44) defbuf(45) defbuf(45)
47 : Dodge defbuf(47) defbuf(48) defbuf(48)
49 : Lucky defbuf(49) defbuf(50) defbuf(50)
-------------------------------------------
01 : Brawl enhancement(01)
01 : Sprint enhancement(01)
02 : Rest enhancement(02)
Thanks for all the help
So after playing around with it for a while (the build, cheeky 
), I've come up with...
01 : Focused Fighting defbuf(01) defbuf(5) defbuf(13) endred(17) endred(37)
01 : Storm Kick acc(01) dam(3) dam(3) dam(7) endred(19) recred(34)
02 : Cobra Strike acc(02) disdur(7) disdur(15) disdur(25) endred(25) recred(37)
04 : Focused Senses defbuf(04) defbuf(5) defbuf(15) endred(17) endred(37)
06 : Jump Kick acc(06)
08 : Crane Kick acc(08) dam(9) dam(9) dam(13) endred(19) recred(40)
10 : Practiced Brawler recred(10) recred(11) recred(11)
12 : Swift runspd(12)
14 : Super Jump jmp(14)
16 : Dodge defbuf(16) defbuf(43) defbuf(43)
18 : Health hel(18) hel(50) hel(50)
20 : Stamina endrec(20) endrec(21) endrec(21)
22 : Crippling Axe Kick acc(22) dam(23) dam(23) dam(29) endred(31) recred(48)
24 : Focus Chi recred(24) recred(29) recred(48)
26 : Dragons Tail acc(26) dam(27) dam(27) dam(43) endred(45) recred(46)
28 : Aid Other hel(28)
30 : Agile defbuf(30) defbuf(31) defbuf(31)
32 : Eagles Claw acc(32) dam(33) dam(33) dam(33) endred(34) recred(34)
35 : Evasion defbuf(35) defbuf(36) defbuf(36) endred(36) endred(48)
38 : Elude defbuf(38) defbuf(39) defbuf(39) recred(39) recred(40) recred(40)
41 : Aid Self hel(41) hel(42) hel(42) inttim(42) inttim(46) recred(46)
44 : Lucky defbuf(44) defbuf(45) defbuf(45)
47 : Quickness runspd(47)
49 : Caltrops slw(49) recred(50)
Now I know jump kick isn't great (from what I've seen, anyway), but it is another attack that I desperately need until I can get CAK at 22.
My only concern is that I've left focus chi and quickness too late...
What lvl are you at now?
I think Focus Chi at 24 is a bit late, but it can be done. Quickness at 47 however....I don't know, I wouldnt do this personally! (I LOVE quickness)
I say drop aid other for quickness, and get the medicine pool in your 40s. That's just me tho.
And yes, Jump kick is indeed horrible....another thing I wouldn't do :P
I don't know this for sure as my MA/SR is low lvl, but from what I have heard with quickness, and 3 slotted recharge in Practised Brawler, does the effect of PB not over lap? I understand it does, and thus offers perma mez res in a form that can't be detoggled, which would mean quickness would be vital asap.
3 slotted PB (with SOs) is perma by itself. As a matter of fact, you just need 2 recharge slots in PB to make it perma, with or without quickness (IIRC). I am 100% sure that with quickness and 2 slots it overlaps too.
Oh yeah, I just 3 slotted PB on my lvl 13 MA/SR with recharge DO's, and herostats shows a down time of 12 seconds, so I can fully believe now SO's cover that. Still quickness has a nice recharge on it for all your powers, and I will be sticking it in well before the 40's.
I'd consider getting haste and getting it early, possibly with SS at the expense of jumpkick and SJ. I found it more useful to have the big attacks cycling quicker than to have an extra low level attacks. I seem to remember when haste is running you can have a constant attack cycle with just Eagle claw, Dragon tail, Crane kick and Storm kick.
Lastly, you'd be supprised just how awesome the presence pool is for a scrapper.
I find that I have PB perma with only 2 SO slots. But then i have Quickness 3 slotted.
MJ
[ QUOTE ]
I find that I have PB perma with only 2 SO slots. But then i have Quickness 3 slotted.
[/ QUOTE ]
If I remember correctly there is no need to slot quickness as it only increases run speed. 2 SOs are enough to perma PB, 3 gives a nice overlap if you can spare a slot. Suggest to take quickness sooner as well - in fact as soon as possible - although with all the good stuff in MA/SR its difficult to fit it all in. Pushing passives to later is how I did it.
UNION @Flitz 50, Lead Hose 50, Red Rag 50
DEFIANT Rose Bloodthorn 34
VIGILANCE Captain Caledonia 20 - Yeah, I made toons on the French server coz we only had 4 back then (might have to transfer/recreate them on one of the US servers)
..and many more!
So, I've finally decided to go back to my scrapper after she has sat in limbo for the past year
Here's what i was thinking,
Archetype: Scrapper
Primary Powers - Ranged : Martial Arts
Secondary Powers - Support : Super Reflexes
01 : Focused Fighting defbuf(01) defbuf(7) defbuf(7) endred(19) endred(43) endred(46)
01 : Storm Kick acc(01) acc(3) dam(5) dam(11) dam(31) endred(40)
02 : Thunder Kick acc(02) acc(3) dam(5) dam(11) dam(31) endred(42)
04 : Agile defbuf(04) defbuf(15) defbuf(19)
06 : Combat Jumping defbuf(06)
08 : Focus Chi recred(08) recred(9) recred(9) thtbuf(43)
10 : Swift runspd(10)
12 : Crane Kick acc(12) acc(13) dam(13) dam(15) dam(37) endred(42)
14 : Super Jump jmp(14)
16 : Dodge defbuf(16) defbuf(17) defbuf(17)
18 : Health hel(18)
20 : Stamina endrec(20) endrec(21) endrec(21)
22 : Focused Senses defbuf(22) defbuf(23) defbuf(23) endred(25) endred(43) endred(46)
24 : Practiced Brawler recred(24) recred(25) endred(37)
26 : Dragons Tail acc(26) acc(27) dam(27) dam(31) dam(34) endred(37)
28 : Lucky defbuf(28) defbuf(29) defbuf(29)
30 : Quickness runspd(30)
32 : Eagles Claw acc(32) acc(33) dam(33) dam(33) dam(34) endred(34)
35 : Evasion defbuf(35) defbuf(36) defbuf(36) endred(36) endred(46) endred(42)
38 : Elude defbuf(38) defbuf(39) defbuf(39) recred(39) recred(40) recred(40)
41 : Kick (Fight) acc(41)
44 : Tough damres(44) damres(45) damres(45) endred(45)
47 : Weave defbuf(47) defbuf(48) defbuf(48) endred(48)
49 : Focused Accuracy thtbuf(49) endred(50) endred(50) endred(50)
Now, let me just get this straight. I know absolutely nothing about scrappers, I've played one for about 8 levels and that's it
So, any advice would be greately appreciated.
Oh and please don't laugh too much