I didn't have my input splines hit the pilot bushing like you did, the input shaft hit the bottom of the crank pilot hole when I tried with the shorter bellhousing. But, that was on the old motor, the block and crank are different on this one and I've now learned a good lesson to recheck E-V-E-R-Y-T-H-I-N-G.
I got the motor torn down to a shortblock. I'm not going to pull the cam or the piston assemblies. I'll have the machine shop do that and when they are done reassemble the short block for me. I did find some interesting things in the process. Top of the motor looks clean, no chunks of any bearing material found anywhere.
Roller Rocker adjusters and Pushrods
The adjusters on my Comp Cam roller rockers look..not so great. There are two that were bad enough that when rotating the pushrod around it had a few stiff spots in it. The cup of the corresponding pushrods looks like it wasn't rotating and was starting to cut a trough. Looking at the other adjuster balls...I'm not impressed at all with the quality here. These should be perfectly round and it looks like when they are made they just cut off the bottoms of them and don't de-burr the edge that is created there. I think that edge caused the problems here. I'll order new adjusters for all of the rockers and a few new pushrods from Smith Brothers to replace the ones that look suspect. Looks like a problem caught early here, which is good. If anyone has a recommendation for better adjuster screws that work better, please let me know.
Valve tips
The valve tips have a wear pattern in them already after only 2hrs of total run time and no rpms above 2500. The wear pattern is centered over the tip, which indicates proper pushrod length, however I can barely catch my nail on the edges of the wear pattern. This doesn't seem right. Should the wear be so deep so fast?
Cylinders
This is the scuffing I was seeing from the bottom end. None of it is deep enough to catch a nail on, looks about as deep as the honing. I didn't pull the pistons, so I don't know what the rings or skirts looks like, but hopefully it is all reusable with just a honing job.