If I were you, I wouldn't look into fuel issues just yet. It has an upgraded Walbro fuel pump. If you just need a working car, this isn't the car for you.
I've learned that the hard way. I will never buy a modded car, or mod a working car, unless I am prepared to deal with it (need time, space, money, and a troubleshooting mindset) from now on.
Now for the helpful troubleshooting part of my post:
My last dealing with this car was the IC itself was punctured, which introduced an open circuit for the air. After that was replaced, I was still having issues pointing to air leak, but didn't have the time or the money to bring it to a shop to do a leak test.
There were two leak points I've fixed - the IC (replaced), injector o-ring (found by spraying engine cleaner). The shops charge too much to get it tested each and every time, plus parts, so I sold the car - just can't afford it. If I had the time, money, and workspace, I would have loved to continue troubleshooting the car.
You don't want to deal with too many things at once, or you won't know what caused what to happen, etc. First, lets work on the intake side - make sure there is no air or vac leaks. Get it pressure tested.
It's been a while since I had the car, so while I did a compression test, what was good then may not be good now, so go check that.
If that all checks out, make sure the fuel pump is still good - just because it's been upgraded doesn't mean that it isn't failing NOW. Make sure fuel filter isn't clogged while you're in there. I had a fuel pressure gauge installed for this purpose. Unless the previous owner removed it, it should still be visible under the hood by the brake fluid tank.
Get as much documentation as you can about the car (service manual), the boost controller, and the SAFC. We will be looking into electronics and wiring issues here. I'd blank out the SAFC for now (make it just a pass-thru device just for monitoring ONLY). As JP said, the boost controller isn't very user friendly, and while I found out their cryptic way of tuning, relaying that info to the shop owner was futile. I don't remember how it all works now - it's been a while, so please don't contact me regarding the specifics of tuning with that boost controller. Sorry.
Re-check wiring on the ECU. I think it's mostly correct except for one or two wires that JP figured out after I sold my car. You may need to send it back to JWT to get it tested - make sure all modules are still functioning as JWT intended. I heard somewhere that someone fixed a check engine light this way (a code specifically for EVAP or something like that) on this very car. Perhaps with all this tinkering, something got shorted and fried that part of the module again.
The transmission was good when I had it. The only issue I had was the spring popped out on the shifter. It was kinda hard going into 1st, but other than that, I loved it. The stiff clutch I got used to - I loved the low biting point. I have no advice to give on it.
In my experience, it is not wise to try to tune the car until you checked out everything. Everytime I did troubleshooting, I'd find a problem, and I would think "that fixed it", and took it to tuning. Of course it doesn't work out, and I had to spend more time troubleshooting. In the mean time, the shop earned their money for me taking the car in just to ATTEMPT to tune.
So Cliff notes:
I'd focus on plugging up the air leaks, making sure there's no leak, then continue looking into the fuel delivery system. If all is good, check wiring and the ECU itself (send it to JWT for testing). Hell, you can even remove the SAFC to have one less thing in the mix. I'd even go a little further and check for exhaust leaks before I finally take it in for tuning.
If you don't want to go through all that trouble, you can try dropping it off a performance shop and say "I just bought this, I dunno what's wrong with it, check it out, and get it running" and see what happens.