For the amps I'd pick one of the two Boogies. I can't say which you should get since they're so different. They're both fantastic though.
You should check them out yourself at decent volume, and spend a bunch of time trying both amps. Also remember to be very delicate when turning knobs, as the slightest turn can make all the difference. You should also try them with good cabinets, as the stock speakers in Mesa combos aren't very good IMO.
The Mark and Recto series are very different amps. Mark amps are tight, crunchy, smooth, and liquid-y. Recto amps are very loose, open sounding, and very gritty and dark sounding. For the most part.
For a good example of a typical Mark sound, listen to Acid Rain and Another Dimension by Liquid Tension Experiment. Both of those songs have great Mark lead and rhythm sounds. Oh, and everything on Liquid Tension Experiment 2 is Mark IV, and Mark IIC+ (I'm pretty sure).
For a great Recto Tones listen to anything on Train of Thought. The Glass Prison is also another track with great Recto tones on it.
As for the pickup thing, I've tried both, and IMO the Steve's Special is the better sounding of the two. It's a lot clearer and tighter sounding, and (again, IMO) also works better for lower tunings. I think you should try your best to try both out, because you might think totally differently than I do, and prefer the D-Sonic.