Sorry to hear about your fuel filter debacle. 3rd gens have it halfway between the engine & tank with nothing obstructing it.

Your engine break-in procedure is very similar to what I did for when I put my performance cams in. Zinc oil, run it for 20 minutes, drain oil, run it easy for 500 miles then go to town and enjoy it. Adding the transmission break in on top of it does sound pretty complicated though.

Starting it up after a replacement is the most nerve-wracking experience I've yet to experience working on a car. You want to start it up, but at the same time you don't because you don't want anything to go wrong! Maybe I can just turn it into a 1000 lb paperweight...