I might suggest scrapper then, since he's a martial artist.
Katana/Inv would seem to fit well, or you can just go for bare fist and inv.
the real name I leave up to you.... (maybe Larry?) but the hero name... Hmm.... "Bio-Mech", "5 of 8", "Cogswerth", "Heavy Gear", "(The) Rage Machine"?
SG name: "The Bio-Mechanicals"
ps, what do you guys think of the story?
and all suggestions are welcome
The story? Well clockwork robots arent that pretty looking. I would go for one of the other villain groups that have robots or cyborgs. This includes Council, Crey, Freakshow, and Malta. Although Malta robots are.... not small. Any other groups that have robots I am missing?
I would definately go for a scrapper. Either Martial Arts, Dark Melee, or Katana. Dark melee has that black cloud stuff but for my character who is like robocop I just say he has vents on his arms that disburse tear gas. Invuln or super reflexes for the primary, is he tougher or faster from the robotic parts?
For a name, think of his personality, what would best describe it? If all else fails use a real name. I have two with real names, Jonathan Kimber, and Paul Barer (Yes I know thats not the correct spelling). Only you can really name him.
Good story.
He's definitely a scrapper. I would say Martial Arts considering his background. For the secondary power set I'd suggest either Invulnerability, or Super Reflexes, depending on what type of benefits the robotic parts provide.
Invulnerability is your Superman-ish set. Gets hit a lot, but takes little damage. Super Reflexes is kinda Spider-Man. Very quick and hard to hit, at least in theory. 
The name is much trickier. This may sound exceedingly cheesey but Stephen Steele popped into my head as I read the story. He has a new power core so Iron Heart seems fitting, but it's probably already taken.
Although, considering he lived so long as a normal human, its hard to picture him taking on a typical Hero-type name. So maybe he would keep his original.
Maybe not much help, but hopefully I can spark an idea or two for ya. 
The Cogs harvest scrap and junk, so if "Junkyard Dog" isn't taken, that's appropriate.
Author of: GOOD TASTE: A Frequent Die-ers Guide to the Turf, Sand and Carpet of Paragon City
I'll have to agree with Bloodwolfe and say that the Clockwork is least likely to perform cybornetic experiments. They're just glorified wind-up toys. Unless he had some metal or parts in him before (pace-maker, artificial hip, hook for a hand, etc) then they wouldn't touch him and just steal his watch to tinker. However, if you want to incorporate the clockwork into your backstory, then I'm sure it can be possible.
For powers: An MA/Inv (or SR) sounds ideal, but I'll list other choices. But, I see him more has a brawler, not a kicker. Maybe Dark Melee (say the black gas it a result of his power source, and get a cover up aura for his arms around level 30). Claws is a nice choice.
If you want to be a Tank, try Inv (again) and either Energy Melee or Super Str. If you want him to be really super strong. Other routes is an Elec/Elec blaster, but since you played a blaster before and might try something different. There's nothing that suites a Controller's or Defenders powerset. Maybe Rad/Elec for a defender, but that's a strecth. Pick the AT/Power that you want to try.
Names: I like the names: Cogsworth. Junkyard Dog may have been taken. My other ideas are: Scrap Iron, Junkyard Man, or Clockwork Steel.
Just brainstorming for fun - some name ideas:
Martial Cog
Clockwork Ninja
Kung Fu Cog
The Karate Cog
Ornithopter Kensai
Shogun Knight
Clockwork Hero
The Clockwork Fist
Hong Clock Fuey
Black Belt Fury
The Reborn Warrior
The Animatronic Ninja
The Clockwork Saolin
The Clockwork Monk
Hong Cog Phooey.
Sorry.
Hmm...
clockwork
The horologist
Pendulum's Swing
Grandfather clock
Past-time
Hope's Mainspring
A little creeped out about this.
That's the heart of Cogged Avengers's backstory. *meep*
Well, that the clockwork did nasty things to him at least. *grin* 28 levels and climbing
I don't see anything wrong with using the clocks. If it were me I'd keep it just because people objected. heh.
Names huh?
The Grey Revenger
Cane of Justice.
Wrinkles of doom.
lol
Okay, I'll try to be serious. 
Cybermonk is all I can come up that's serious though, and I'm sure someone took that.
One more.
Shao Lin Clock?
Good luck with the name thing.
hmm...how bout this?
Gear of the Timeless
or
Cog Infinitum
yesterday this background story popped in my head for a toon:
it begins with a normal guy, in his 50ies/60ies, teaching various forms of martial arts (nowhere on a superhero level mind you).
One day when he walks home after work he spots a girl being attacked by clockwork and he tried to rescue her. (a paragon citizen pff he should've known better).
Ofcourse he fails utterly being nowhere on the power scale of levels as we know them.
The clockwork don't kill him but take him to one of their labs and start experiments on him. after weeks of torture and medication they even replace an arm and leg with robot parts.
After a few failures of this the clockwork proceed to incorporate a power source in his body and replace numerous internal organs.
When he awakes after yet another gruelling operation he hears blasts and fighting and a group of heroes come bashing down the door rescueing him.
The heroes help him stay sane and himself learning him to move around with his new limbs and organs but he lost his skill at martial arts.. the new limbs just won't work like his own.
After months and months of depression the girl he tried to rescue finds him. it turns out she got away and the clockwork were after her for longer. This gives him new resolve and he
starts training again.
It turns out though the limbs and organs work differently they are much stronger than normal steel and somehow the power core in him empowers him beyond normal human strengt, even strengtening and fastening his blows and movement.
a new hero is born in paragon city....
Now i'm planning to make him old looking, grey, not too large a scarred man. displaying various robotical parts on him aside from the leg and arm a bit depending on what is possible.
i'll vary the arm and leg with true robot ones or even armour over the four costumes to reflect the changes he'll make to his limbs and his growth in stength over the levels.
(progressive costumes really complete a story for a hero)
but now the questions.... i need a name...
and what would you guys thing a fitting AT and powersets?
i only played a blaster up untill now and i'm not too much at home in the other powersets to suit such a specific story.