All right guys...So, it is possible I just need a tune but before I do that I want to see if you guys have any idea what else this problem could be.
I bought my Automatic Transmission '04 WRX maybe 18 - 20 months ago...It ran fine for the most part when I bought it. I had afull 3" exhaust on it when I purchased it...but I had some funky CELs due to this stupid ECU I got with the car. To make a long story short, I ended up putting the stock exhaust back on, and also replacing my O2 sensor, and also buying a new OEM ECU from Subaru. Car was running all right, but I would get boost spikes, and it sounded like I had a boost leak. This was really pissing me off so I had it brought to the shop...They found a hole in my intercooler piping which I "sealed" to the best of my abilities seeing as the damn perrin intercooler piping is like 400 bucks for one piece. It was still being weird, but at least it wasn't stalling out anymore. So...my problem remained that the car will fluctuate in RPMs at idle when the car first starts. From about 500 to around 950 or so. Up and down, up and down. While I am driving, when my foot is down on the throttle, and I relax a bit, and then bring my foot down on the throttle again it feels like it wants to sputter, and it like bogs a little or something weird.
So, I put on a new Downpipe...QTP 3" with electric cut-out....I get it all installed...and HOLY CRAP! My car is no longer boost spiking...I have NO turbo lag at all almost, it stops bogging down while I am driving...and everything seems pretty damn good. I was driving down Route 7...and put my foot down real good...Push 20psi of boost and take off like a bat out of hell. I slow up....drive for a little bit and notice that it feels like there is that good old turbo lag again....So, as I'm almost home I put my foot down to see what happens...and boost spiking 15psi down to 10psi and back and forth really quickly. The car is starting to bog down when I am driving normally, and it's idling really low when I start it and its jumping form 500 - 950 or so again.

WTF could this be? I'm assuming a number of problems....some ideas I have so far....
Torque Converter Clutch going bad?
Fuel Filter Disgusting?
I'm at a loss....Any help would be greatly appreciated. Thanks ahead of time guys/gals.
P.S. I have a CEL on that says I am running too lean....but that has been on for a while...I guess I should clear it and see if it returns.