And the day has finally come, it's fixed!
 

After about 2 years of searching, spending money, and trying to figure out what was wrong with my car, the one thing that EVERYONE said to change, and I knew I should've changed first was indeed the problem. So if you have these codes,

P1688: Manufacturer Contrl - Auxiliary Inputs/Auxiliary Outputs
P0107: System too lean (bank 1)
P0171:MAP/BARO circuit low input

CHANGE YOUR MAP SENSOR IN FORNT OF THE IC!

I had a lot of other work done as well on my car from a mechanic at Clear Lake Advantage Mini and without him I don't think the car would be running the way it is now. Yes that sensor was the majority of my problems, but without all the work he did, I'd still have a lot of issues.

As for my misfire in cylinder 3, he fixed all my vacuum lines, replaced the coil pack, and the misfire was still there. I later switched my wires from cylinders 3 to 4 before I did a compression test one day and BOOM! Cylinder 3 was fine and cylinder 4 misfired! So today I replaced my wires with some 8.5mm wires. I've also done a sea foam treatment. As of now, there is NO MORE stutter or spitting, it's fast reacting, A/C doesn't bog down my idle too much, and overall the car drives like a car should! I am still blown away with the way it's driving now! Thanks for everyones feedback and continued help and support involving my problems on the forum, without you guys I wouldn't have gotten very far!

Only problems left,
Power Steering Pump (which I already have) PS Fan, Radiator low speed fan, and my oil pan gasket. The mechanic said the oil leak may be coming from the seal around the oil dipstick.

Oh, and it's still not fast enough :D lol

Here are two videos, one of my last sea foam treatment, and one video of me trying to hear what my exhaust sounded like with my GoPro cam suctioned to the bumper and it fell off while driving! Just thought these were great!

Also, here's a new picture with my blue wires I got! Used to have red!

http://img254.imageshack.us/img254/1071/img1598c.jpg

Your pan gasket is probably not leaking, it's either the crank sensor o-ring or the dipstick o-ring - or both.

Which are both a PITA to access coincidently

I like those blue wires!

Thanks!

Was your Mechanic Tony or David? Both of those guys and Lance are pretty awesome. But tony recently left and is now at porsche. Tony actually came out to my house a couple of times to help me out about a year ago.

right now I'm throwing
P0171 Lean bank 1,
00564 (0234),
p1237 Intake manifold pressure sensor low input.

and have a leak coming from in between the trans and engine

Haha! Yeah I work with Tony! He does all my work still over at Audi/Porsche! That sounds like your Map sensor to me!