Nice buy!
B6 chassis is a good A4, one of my favs (aside from b5 S4s and A6 2.7 bi turbo)
i should start by saying, i work at an independant german car repair shop (with quite the rep... not the point though), so i see Audi and VWs all day. I have worked on a LOT of 1.8t equipped cars, both transverse and longitudinal layouts.
things you should watch for:
1) timing belt, if your car has never had it changed, for the love of god, GET ONE! 75k/5yrs change interval. i have seen them strip teeth and just flat break on cars with 50,000 miles or less because of age (the first one i saw i think was an 01 TT.)
2) oil leaks, chain tensioner housing gasket (chain between the two cams), valve cover gaskets, cam seals, and less likely oil pans (no gasket, just sealant)
3) CEL for "cooling system performance malfunction", most likely the engine coolant temp sensor (G62), lately though, i had two jettas, one a 1.8t ('03) and one a 2.0L ('02), very persistant error, it took a thermostat and a temp sensor from the dealer to solve the problem. so the best bet is to do the both at once, maybe 1 hr of REAL labor.
4) worn out front end parts, the multilink suspension parts open up a lot of opportunities for worn out ball joints (4 per side, not counting outer tie rod ends), i see more on B5 chassis and mk2 passats, the b6 A4s havent been showing too much yet, still pretty new.
5) Air Mass Meters, they suck, but the price has dropped, so whatever, be prepared if you want to run an oiled air filter (K&N kinda sucks anyway, the Mahle paper filter is supposed to flow more anyway)
6) vaccuum leaks, usually just a dried up hose or a black/gray check valve that has deteriorated (the outside of the case literally rots off)... audi/vw failed at materials for these littles dudes...

As far as GIAC v. APR, well, let me just point out that, this year, APR doesnt seem to be able to take a car all the way to the end of a race because of blown motors...
a coworker has a B5 A4 with a 1.8t and GIAC software, and it really woke his car up, it will spin in 2nd gear (fwd only), added ~40hp+.
he went to Eurotech tuning and got his car flashed, I couldnt really recommend any shops for a reflash because i don't have experience with them, but i hear scott (at eurotech) is a cool guy.