well for starters your stock turbo has a ceramic turbine wheel meaning that it cant take the heat generated from high boost at WOT for extended periods of time... Your garret turbo will have a steel wheel however depending on which turbo you have your center section may not be ballbearing, most probably journal bearing meaning that it will be less efficient. Keep in mind that most oem turbo equipped vehicles do come with journal bearing turbos so its nothing to worry about. If your exhaust housing is 4 bolt youll need to find a nice 4 bolt flange and weld up a custom down pipe. Getting braided lines fitted to your turbo is alot easier than working with those horrible hardlines so id highly recommend it. Its easy to do, just take the fittings from your block out and bring them in with your turbo to any high pressure industrial fittings supplier, tell them you need some braided lines made, it should be easy enough!
Goodluck,
Chip