Wow, this is fantastic reading. Sorry, that was sarcasm. If you are able to feel scratches in the bearing, can you do the same on the crank journal itself? If so, crank needs turning or you will be doing this same job in less than a year.
1. What are you talking about? Did you grind out the metal windage tray and get metal filings all over the place?
2. Start with the rod bearings first, and if they are bad, it is best to check the main bearings, and at this point, if the rod bearings and main bearings are bad, so is the crankshaft, which needs to come out and be turned, thus it would be an undersized crankshaft, so no, standard bearings won't work.
3. Permatex is not expensive, slight nicks are the main reason for using it, clean the surfaces really good.
4.Try the dealership for the bolts, or a salvage yard to pull some off another 3.5 engine.
5. To get the bearing shell out, look for a tab, push with your thumb on the other end of the rod cap and it will slide around the curve to the tab, then pull it out. Top and bottom halves can look alike, but not always the case.
6. There is a bolt on the harmonic balancer on the front of the crank. Use that and a ratchet to rotate the engine. If you pull the sparkplugs it is even easier. Be cautious not to jam a rod end into the journals of the crank, it will damage it.
7. Depends on the condition of the crankshaft as noted earlier.
8. Tri-metal or Clevite 77 bearings are far superior to other single or metal clad bearings.
You wouldn't have a car buddy you could communicate with on the spot, maybe answer some of these questions on the spot, not that we can't help or anything, might just help with some of the answers a little faster.