Excellent question...I've debated the MX6 vs MSP in STX with Gavin a couple times...he thinks that equally prepared to the rules it would be a toss up, and come down to the driver. Given the added HP to be made by the MSP with Boost, albiet heavier than the '6 and the fact that suspention and tire offerings are quite similar...It may very well be a tossup again...
Ryan: your car seems similar/identical to what I'd be looking to do. Are there any parts or things you would have done differently a second time around? or are you still in the testing stage?
Always ALWAYS testing

Done differently? Sure, I would have spent more money on the suspention likely with Koni DA's, or possibly a KW setup. I don't regret the TEIN's, for all my knowledge they've worked very well, and very reliably so far, however I do somewhat feel I'm getting to the point that I can take advantage of a double adjsutable strut, instead of just a single adjsutable. Other things? Not much.
Also, I assume I should look for the V6 LS model. Were these made without sunroofs and spoilers? Any specific year that was better than others? How reliable are these cars (it wouldn't be a daily driver though, I have my BMW)?
I would most certainly recomend the V6, you'll be able to make gobs more power than you ever will with the four cylinder, and weight difference isn't that great since the FS 2.0 is an iron block, where the KL is all aluminum. You can find them without sunroofs or spoilers, but the ONLY ones I've ever seen without sunroofs were very very early '93 vehicles, with production dates in 1992. Non-Spoiler ones are slightly less rare, again more '93's came without spoilers, however it's always an option to be rid of it, and put a 3rd brake light in the rear window, which is what I've done.
If you wanted the absolute lightest, you would want a non-sunroof, non-abs, non-spoiler cloth interior early production '93. The HP and TQ numbers are slightly different as well. The '93 is rated at 164hp @6k rpm 15Xtq @ 4500rpm while the '94+ is 164hp@5600 160tq@4000 IIRC.
Reliability? In my own experience of owning my 4th MX6 LS, (not including my Sister's) and multiples of it's chassis mate the Ford Probe, they are VERY reliable. The biggest problems I've had are with distributors, which are common to many early '90's Japanese cars. I've replaced as many distributors on Honda's and a few Toyota's as I have my Probes and MX6s
Would it be better to stay OBD-I?
I'd most definitely recomed staying OBDI, as putting headers on the OBDII model eliminiates the Pre-Cats and you still have to deal with the secondary 02 sensors which are there to monitor catalyist efficiency...in other words permanent check engine light with the pre-cats gone...And you still have to weld extra bungs in the headers for the secondary sensors.
Did I miss anything?
Oh, and here she is in her element, on track at Miller Motorsports Park straight Piped and some nice clips of AutoCrossing
http://www.youtube.com/watch?v=LQIa4k_S0MI
Ryan