Joe, the best thing to do in your situation, is to really sit down plan out your goals, figure out what parts you want to use to get to your goal, then figure out who is going to tune it.
Your best bet is to discuss the diffrent features of the ems units your tuner is most familiar with, select the one that incorperates the features you will get the most use of, and have your tuner tune it.
just to expand on the great post by st205wrc above me,
he covered pretty much all the basic bases as far as some of the most popular EMS units used on the 3s these days.
the key, like everyone here is saying, is using a unit that whoever is tuning the car is familar with, that way your not paying someone to learn how to get the most out of the software available to them.
being in texas, i would shoot a call over to aaron and the guys at ATS racing.
they are without a doubt one of the more experienced 3sgte tuners in the country, with lots of options as far as powergoals, and what not.
there are a large handfull of guys over on mr2oc that are running ATS kits, making 350-450WHP without a problem using a handfull of diffrent turbos, from the td06 to the gt3071, precision 5857, ect. alot of them use the power fc, its reletivly cheap, the guys @ ATS are very experienced with it, so tuning it for them is a breeze, and it just works.
here are a few threads i pulled up on mr2oc where guys show the results of theyre builds, most of them are tuned by ATS, using the powerfc.
this guy is running a stroker build, and gt3071:
http://www.mr2oc.com/showthread.php?t=4268...;highlight=3071heres one with a TD06 kit and AEM ems:
initial tune:
http://mr2oc.com/showthread.php?t=426788dynojet retune:
http://www.mr2oc.com/showthread.php?t=4275...;highlight=3071another 3071 + powerfc, tuned by ats
http://www.mr2oc.com/showthread.php?t=3377...;highlight=3071and a precision 5857 (same turbo jim is using on the 5sgte build i am doing for him, check out my "building a big bore stroker" thread in the FI section for more info)
http://www.mr2oc.com/showthread.php?t=4074...;highlight=5857there are tons of build threads like this on mr2oc to refrence from and get an idea of what diffrent turbos do as far as powerband ect with diffrent setting and mods.
the one constant in all these threads are they are all tuned professionally, by someone who is familiar with the software and the engine.
good luck dude!