Good guide, just some notes I can throw in off the top of my head...
1. For a Master run, try and get as many people on the team as possible on either Ventrilo or Teamspeak or something along those lines. This makes such a huge difference
2. The ambush in Mission 1 doesn't always come from the right. Most of the time it does, but I've seen it from the left, behind, and from down the ramp. Also, before destroying the last part, before the cutscene, I will throw Spectral Terror down on the stained patch of ground at the top of the ramp. That way, when the cutscene ends the mob already has a fear thrown at it.
3. Make sure in Mission 1 that everybody knows how many parts to leave, and not to destroy which ones before you start. Also, some teams may not do it this way, but we always exit immediately as soon as the Exit button pops up. Some people may not know to do that and can lead to a death real quick.
4. If ghosting to the thorn tree, at the section with the waterfall and the named bosses, one of them sets up seeker drones which give the mobs +perception. Not sure what level of stealth they can see through as I haven't tried testing that very extensively, but they have spotted our ghoster before. So just keep this in mind if ghosting on an MSTF run.
5. For defeating the "Security Chiefs?" we usually send 1 blaster and 1 emp to blitz the Chiefs until the key is found, then the whole team rushes to the door to wait out all the ambushes. For this part a targetting macro or bind is very handy. I don't know the macro offhand, but I just bind to the letter g with:
"/bind target_custom_next security"
6. The ambushes after you get through the door will spawn mostly under the ramp, but they will also come from the doorway at the bottom of the ramp, or I've also seen them spawn under but then rubberband to different parts of the room. We've even taken out the first AV and had them spawn on the second floor. So make sure to watch out for more than just under the ramp.
7. Ghost Widow and her holds are probably the most dangerous part of this TF from my personal experience. CM on the main tank is very very necessary for her. Our stone tank has been held through 5 CMs and 2 Clarity. From what I understand 8 is enough, but not 100% sure on the mag she can stack up to, so more is better. Also, she can cage your tank, so it won't be able to taunt. Very important to let the team know as soon as it happens, otherwise they can peel the aggro off while the tank is "Only Affecting Self". One last note on Ghost Widow is that she has a PBAoE heal, so the more toons in melee range of her, the more she will heal off of them, so keep everybody back from her (except Phantom Army...her heal doesn't work off them so they're ok)
8. Scirocco....well, there's a reason that he has a PBAoE set named after him. Keep squishies out of melee and behind him. His cone and Lord Recluses are perfectly capable of 1-shotting them. (Recluse can take most scrappers to 1hp with his)
9. Mako has a tendency to go a little crazy and run off and attack a squishy real quick, then go back to hang out with the tank. He's just weird like that.
10. The Flyer is on a respawn timer. I forget offhand how many minutes it is, but if you're lucky it will respawn as soon as you start fighting it, so you know that it just respawned and you have the max time to take Recluse out before it comes back.
11. Make sure you take all the mobs out that are in the square under the Flyer before you start on Recluse. Otherwise they WILL aggro when you start taking out the towers on their side of the map.
12. As soon as the tank gets Lord Recluse aggro'd have a rad throw one of their debuff toggles on him. Otherwise he will start spawning all his Bane Spider bosses and eventually he can get enough of them spawned to where taunt won't be able to keep them all aggro'd. I've heard that any auto-hit debuff works to do this, however I haven't personally confirmed that.
13. (And I was so trying to keep this in order with the STF and I forgot this one) We have started having a blaster get the glowie from the thorn tree. They seem to have much better success with it not missing than our stone tanks usually do, but as you said different teams prefer different things.
And lastly, our usual team is 1 stone tank, 1 kin, 1 or 2 emps, 1 or 2 rads, 2 blasters and depending on how many emps and rads up to 2 of anything else.
Overall, great guide. Most of what I've thrown on here is just personal experience and preference of how we run ours. Didn't mean for it to wind up nearly this long, just wanted to throw in the things we normally warn first-time STFers about on each mish.