Timing, rotors, exhaust, and ball joint!

Hello....My 94 Accord EX just hit 140,000 miles and is starting to show it's age.

First off, the timing is off. Is there an easy way to set the timing using a timing light or is this something computer controlled. When the rotor was replaced, the shaft the rotor attached to was accidentally rotated a bit while the car was off. This would disturb the timing, correct? Timing belt was replaced at 100,000 so no problems there.

Next up, the front rotors are done. When I have my mechanic do these is it a good idea to go ahead and replace the wheel bearings?

My center pipe exhaust piece has a hole. It looks pretty straightforward to replace...loosen or cut the bolts and install new hardware...anyone have any experience doing this? Any pitfalls?

Finally, the only real non-maintenance problem....my ball joint on the front driver's side went out (common problem). I had it replaced but I think it is going out again after ~200 miles. The symptom is a whumping/thumping/clanking noise when I'm coming out of turns. In previous cars, when the wheel bearings were going the car made the same noise. But in this car, when the original ball joint was dying I heard the same whumping noise. After replacement, the noise went completely away or was so faint I could barely hear it. It seems to be getting louder now. The mechanic who replaced it test drove it with me and said he could hear it but since nothing was loose suspension wise there was nothing he could do until it got worse.
He did mention the wheel bearings which I also suspect but did he say that just because he didn't want to look at a warranty ball joint job? As I mentioned, after the new ball joint was installed, all the noise seemed to go away.

Thanks!