Thanks everyone for all the replies, sorry for not being able to respond to everyone one by one.
The shop I called has been around for awhile, the guy on the phone said they use to do tons of 22R's back in the day, which means they know these things. Which is always good.
I forgot to add, but they would also balance the flywheel too, which is a huge plus. It's a lot of machine work, but I'm taking everything as if it needs to be done, the block might not need as much work as I think, there's stuff you just can't see with the human eye.
It'll be awhile before I get the block and everything else in, I think I'll take the block first followed by the head and then I'll take the rest of the stuff later.
I'll call other places and see too, I'll talk to some of the master techs where I work and see what they recommend.
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Just to add a couple thoughts...
If you have them balance the flywheel you might ask them to balance the pressure plate with it, that was the recommendation by my machine shop. A very reputable Toyota engine builder told me that I didn't need to balance a Toyota Factory crankshaft.
Also, if that shop has experience with 22s, they should know to machine the timing chain cover with the block if they deck it. My shop only needed clean the top of the block deck about .006", but also machined my timing cover to match.
My machine shop recommended a .020" overbore. One very reputable Toy engine builder did not recommend an overbore anymore than necessary. However, if could go back, I'd seriously consider doing a .060" overbore to get a little more displacement - I believe 79coyotefrg built a .060" over. I realize that it may make the block non- rebuildable again, but I don't plan on rebuilding it again, and I realize the cost for .060" pistons is more money. As I mentioned before, if I could go back, I'd rebuild my 22RE and convert it to a 22R - carb... then ask H8PVMNT if he would work his magic on a supertune!
But if I could go back, I'd seriously consider a Chevy 4.3 Vortec... then while doing that mental exercise, I'd probably end up swapping in a V-8!!... I always wanted a V-8 in my Toy trucks. That swap is not completely out of the realm of possibility in the future.