No problems on stage 2 what so ever, have 40,000km on my stage 2 FBO setup as well, and it gets its fair share of beatings. Everyone above is correct. If you were Stage 3+ then you can begin to worry about bottom end stuff but even then, the bottom end is still fine.
Stage 1 to 2 is not really a massive difference in power, more so in the way its delivered. Its stronger up top and pulls harder all the way to redline rather then dying like stage 1 does. The more bolt ons you have with stage 2 the more power you will make but again its not really a massive difference over 1. If you want that crazy OMG feeling again like stock to stage 1 you need k04 or bigger.
Unitronic vs APR is really going to be a personal thing... Both have great software for stage 2 it really just comes down to availability in your area. I've been UNI since day one and had no issues at all, car is really strong (specially in the 1 degree weather we are having now
). If I had to choose for K04 or larger software though? I'd probably head towards APR.... Just my thoughts. Both are good.