Not that it matter anymore, but... I heard another small rod knocking sound on Tuesday after I finished replacing the #5 bearing. At that point I decided to just replace the rod bearings again now that I know I didn't prelube properly the first time.
So on Friday I swapped out the entire rod bearing set and properly pre-lubricated the crank, bearings, & rod with white grease. Additionally, I pulled the distributor plug and turned the engine over for about 30 seconds before starting the truck up to build oil pressure and properly pre-lubricate everything again.
Now the trucks running good. I'll post up some pictures in a couple days of what good and bad xterra rod bearing look like.
I'm pretty sure I could swap out a timing belt now in about 3 to 4 hours total now. It's actually not too tough.
NO, NOT WHITE GREASE!!!. That's not the right one for motors. You HAVE TO USE "assembly lube". You also have to check the gap before the final installation of the bearings. If you've never rebuilt a motor properly before, I think you should leave the bottom end to a professional machine shop to only assemble it. The bottom end is the most critical part of the entire car. You can't just slap parts together and expect them to work. There are tolerances that must be kept for proper long term use.