Larry,
I haven't done this in a very long time , but I remember getting a little creative with the bed of my 46 half ton. I used some tounge and groove or half lapped pine and carrage bolts without the metal bed rails. I also added some cross pieces that sat on the frame to have a place to bolt into. I also remember making some 4x4 blocks out of treated lumber to support the end of the bed. I did ths by cutting to length and drilling through the center. So, to answer your question:
1. I would not bother now, if you are to do a bigger job on the truck later. I don't remember using any.
2. Don't need to worry about if you don't use them. I suspect they were there to prevent squeeking so put them against the metal.
3. Yes. I used carriage bolts. I didn't Counter bore and plug and it looked fine.Counter boring with a plug is fine as well just a little more work.
My bottom line is do what works and meets your standard for looking good.
