Thanks everyone for all the help and advice. I ended up just using the lock nuts the machine shop provided although that one that I was worried about backing off is easier to turn than the others. I may just pein the nut at the threads to help lock it in better.
Tomorrow I have to pull the valve cover back off and seal it up since I didn't apply any sealant to the bottom of the gasket, it's leaking. I also will most likely do the same for the lifter covers too, I didn't replace the gaskets for them, just carefully pulled them off without damaging the gaskets. I have new ones, but these were still very pliable. most likely just add some sealant and they will be good to go.
We gave it an oil change using Valvoline VR1 racing oil that already has a high zinc content instead of standard oil and getting the additive. fresh green coolant. and to get it up and running without the fuel tank installed, we rigged up a boat tank in the bed and ran hose to the pump on the frame. had to drill a hole in the boat tank cap and run a return fuel line also.
Now my son is talking about maybe trying to use that turbo 400 trans I got with the 6.2 diesel I brought home. I need to verify it will bolt up to the engine along with if the torque converter will work for it too. then the hunt for a yolk to fit the trans will be needed to make a new drive line or modify the existing one.
If others have any info on using that TH400 let me know.