Return that muffler asap. 2.25" piping is too small for a FI 2.0, and you got ripped off for that muffler. bad. A 2.5" magnaflow system is 500. A 60mm (2.4") Neuspeed system is 500. A MBS 2.5" system is 500. All stainless steel.
C2's tune is exactly what it's called. It's a tune by a company named C2. It's a reflash for MK4's. You'll need to use their 30 or 42#/hr injectors, and their MAF, but other than that you're good to go and it's better than Neuspeed's tune.
Neuspeed DOES make a tune for their S/Cer, but the C2 tune is much better.
WHP is tough to guess. I'd say about 220hp will be around 170whp.. Maybe. Not too sure, I'm tired and remembering drive-train loss isn't my forte.
Just because you have high miles doesn't mean squat. My friend has a 95 GTI 2.0 turbo with 245k on it.
With 180k, you should be fine with low boost on the Neuspeed S/C kit.
Will an automatic hold up? No. It'll be obliterated. It won't release boost pressure during shifts, so theoretically you might be faster, but maybe for a day. You'll need a 5 speed swap for any FI upgrade on your car.
That is as simple as I can make it, bud.. Check out the thread in my sig for more information about your motor, maybe it'll help you out.