An update of sorts on this issue. For the transmission I ended up swapping to a long-input shaft on the TKO600. This in itself was a big dabacle. I found the short shaft had a mangled bearing cage on it from when it was originally swapped from a long to a short shaft, looked like someone used a clamshell on the cage to press it off and then just pressed it on the short shaft. I notified the shop about the issue as a friendly heads-up and in the end the shop lost all my future business over how they dealt with the situation and how they treated me. Especially when I never asked for a replacement, just wanted "gee, that sucks" apology and nothing more.
I digress. So the long-input shaft was installed. I installed a new bearing on the input shaft, had a shim kit and set the shaft end-play to the nothing-.005" spec in the TKO manual I have. I ended up using an engine hoist and a chain to support the trans with the shaft straight up, worked well. There are 17 roller bearings that live in the back of the shaft that need to go back in place, but greasing them up was more than enough to get them to stick there for final assembly.
Mocking everything back up again showed I was going to be too deep into the pilot bearing with the input shaft. The splines on the input would be below the depth of the pilot face by around 1/16" since the pilot extends beyond the face of the crank by around 1/32" on my motor. Taking the advice of a forum member here, I cut a 3/16" step in the pilot bearing, reduced the stepped diameter to 1.25" so it would be a snug fit into the next step in the 428 1U crank. This allowed clearance for the splines on the input shaft as well as having the original width of the pilot for the input to ride on, rather than just cutting the pilot down thinner.
One thing I noticed when installing the clutch and everything in place is that I know I have much better clutch spline engagement. The spline engagement starts around 1.5" from the trans fully seated. The pilot starts to engage at .75" or so from seated and is A FREAKING NIGHTMARE to get that last push into place. Part of this nightmare I think is because the crank centerline moved .0025 up in relation to the trans due to the block being re-align honed. I reverified the crank centerline to bellhousing alignment and it was .0025-.003 high, which is still in the "less than .005" allowment for the TKO600 to shift reasonably well and not chew up the pilot to bad or cause bad high rpm shifting. The second problem I noticed is that the plastic alignment tool I had was actually allowing the clutch disc to fall down slightly while the pressure plate was torqued down. I again used a forum members advice and used my now spare short shaft as an alignment tool and supported it slightly with a small bungee cord to keep it as level as possible to the crank centerline while getting the pressure plate in place. This made the trans engagement much easier, but it's still a bear getting that last 1/2" to slide into place. I have a feeling with some road time this will get easier as the brand new pilot wears slightly.
Lastly, I ordered up a different set of ARP flywheel bolts that are a smidge shorter than the ones listed for the FE's. These are 240-2801 that are 7/16" x .875 instead of 1.00". With the flywheel in place the bolts are flush with the front face of the crank when fully torqued, so that is much better than having bolts hanging out there in the wind like last time.
I'm feeling a lot better about the clutch and trans now and have learned a HUGE amount with this whole ordeal. Nobody learns this stuff the easy way (unless they read this post and remember it I suppose), but that is part of what makes this fun I guess.
