83' KZ750 F1 Full Rebuild

I've done rebuilds for carburetors, brakes, forks, starters, electrical, wheels, etc. and even replaced my shaft drive all before but looking for some insight into doing a full engine rebuild as anything internal beyond removing the cam cover of an engine and poking around is new to me.

Around 3 years ago one of my rods decided it was ready to explore the outside world while I was on the highway. Luckily I felt something right before it happened and was able to safely pull off. I will admit I hadn't taken amazing care of the engine prior to this happening which you can probably tell from the pictures below. 



I was able to get another complete engine that appeared to be in decent shape but upon getting home realized the extrusion on the lower half of the crankcase that held the shift lever and spring in placed was broken off so I got another crankcase. Got everything disassembled a couple years ago but stopped for a while and let everything sit while life continued on. My girlfriend recently got a Honda Shadow and I got back on a bike for the first time in 2 years and realized how much I missed it and am ready to bring mine back. 

My main question is what needs to be replaced/checked for replacement while reinstalling all the internals/what are good practices while rebuilding an engine?
I put off doing this for so long because I'm honestly scared of missing a bad part and the engine getting destroyed again.

Things I currently have/am doing/have questions about:

• I have a new full gasket set along with new piston rings which are the obvious parts to replace.
• As of this week I'm starting to take apart and clean things in lacquer thinner before reassembly like the transmission, oil pump, secondary shaft - but should I continue to do this, with things like the crank shaft and all the rods?
• Should I be replacing the roller bearings that are in the case, the main bearings, and/or the rod bearings?
• I have two complete cylinder heads/top ends, one that came off my bike that I know was working and one that came off the new engine that is mostly a mystery other than visually it looks alright and the guy I bought it from said it ran last time he tried(?), should I use one or the other or mix and match parts to get the best one?
• I'm basically working with two full engines worth of parts, obviously things that were damaged from my original like the crankshaft and directly connected parts are out but what about picking the best of things like the transmission, secondary shaft, etc., or should I stick with keeping all the internals from my second engine for consistency?

Just looking for any advice because I could get the whole thing assembled and running in a week but I could also be missing some major things that I should have checked/replaced/etc that will ruin the engine in a week or a couple years and I wouldn't know. 

Thanks in advance for anything you have to offer!
 

The crank bearing shell sizing involves the size of the case and the size of the crank.  I suggest getting a proper Kawasaki manual for your bike so you can review the crankcase and crank markings to make sure you have the proper shells.

Aftermarket gasket kits are risky.  If you bought Athena with green gaskets I'd replace the base gasket with OEM for sure.

You should pull the valves and replace the stem seals.  That would be a good time to service the head too if it needs it.

There are lots of other things to do so get the manual and follow what they say.  Check bore size, out of round, and taper.  Measure pistons.  Hone the cylinders before assembly with your new rings.  Etc, etc.