When I did the heads on mine, I unbolted the motor mounts and jacked the engine up far enough to get the oil pan off, and replaced the rod bearings. I should have replaced the mains too, though it's a little bit tougher to do with the crank still in place. Not impossible, just finicky. But mine had been driven quite a ways by the previous owner with the water in the oil, and then sat for a while before he put it up for sale so there was plenty of time for the bearings to get wiped. They didn't look terrible, but not great either. There's a decent chance that yours are okay.

If you didn't have any lifter noise problems before, I wouldn't mess with the lifters. The '89 2.9 should have (as I recall) non-adjustable rockers, so there's no preload adjustment needed on the lifters. You can clean or even rebuild the injectors yourself, there are kits available to do that. Not too much involved with the process really, but I'd probably just clean them.

I seem to recall a similar problem with the Fel-pro head gaskets, I don't recall it being any issue though.