I was recently asked how to remove a stock turbo. I almost said just folow the BGB, but there are a few tips that aren't in there. Plus most of us have downpipes by now so here is how I do it:
First, I am assuning you have a downpipe and not the stock elbow/cat assembly.
1. remove any intake/AFM, etc.
2. remove the manifold heat shield. There are two 12mm head bolts on the manifold and one on the turbo. Apply penetrating lube to all the exhaust studs/nuts on the manifold.
3. Jack up the car and safely secure it with jackstands
4. crawl underneath and remove the oil drain elbow. It's rubber on a gen2, aluminum on a gen3. Be careful because the rubber part is no longer available. There is also one 14mm bolt holding the drain pipe to the block. Remove that too.
5. remove the three downpipe botls/nuts and downpipe bracket if you have one.
6. remove the L shaped turbo bracket if you have one
7. get out, lower the car back down
8. remove any wastegate or boost controller hoses
9. remove the bolt that holds the water pipe to the wastegate bracket.
10. remove the two 10mm nuts that hold the water pipe to the turbocharger. Flex the pipe out of the way. If the hoses tear or leak, well they were old and you needed to replace them anyway. This step will leak some coolant so try to catch it. It won't be more than about a quart though.
11. Use a 27mm socket on a gen2 or a 17mm on a gen3, universal joint, a long extension and a 1/2 inch breaker bar to remove the oil feed fitting from above. You can just barely get through in the space that the water pipe used to be in.
12. remove the 7 or 9 14mm exhaust manifold/head nuts. I like to use a cordless impact gun whenever possible as it seems less likely to break the studs.
13. at this point the turbo should be loose. You will probably need help because it's heavy, but the goal is to remove the turbo, maniflold, downpipe, oil drain/feed assembly as one piece. Slide it forward on the exhaust studs and lift. You may have to adjust your technique slightly as the downpipe flange likes to catch on stuff down low.
Installation is basicaly the reverse of removal. Don't forget to top off coolant.