Home build almost complete. On the bench run, I noticed the shaft housing was hot, but only at the very top and very bottom( exact location of sintered bronze flange bearing). You can touch it, but not longer than 10 - 15 seconds. Using a dial indicator the needle moves from 0 to .005, 0 to -.0096.
I think the alignment is fairly close.
Is this heat due to the sintered bearings or maybe something else???
Any advice??

make sure you greased the bushing before sliding the shaft in or now just unhook your u joint and work the grease into the bushing but a little heat is normal. the bottom one is for sure ok because it will be underwater.

1775, did you ream the bronze bushing? IF not do so, if you have already reamed, loosen the four engine mounting bolts. Take the upper housing cap off and slide up to joint. apply grease to shaft housing and it should come out between upper bearing and shaft evenly. If it is not uniform tap engine around till it comes out like a very fine circle. Put the upper housing cap on and do the same to lower bushing. More than likely the bushings need to be reamed. Good luck.

P S
Once the grease comes out evenly around top bushing tighten the engine bolts.

Everything has been properly sized. I had a machine shop work the bearings, install seals and everything. They do top notch work. Everything has been aligned and filled with grease Like I stated, it only gets hot in the location of the sintered bronze bearings on the very end. The internal sleeve bearing locations are not hot at all, making me wonder if it is just the oil impregnated flanged bronze bearings. Just to clarify, I have an oil impregnated bronze flange bearing then 4 seals, 2 face out, then 2 facing in, then bronze sleeve bearing, sleeve bearing in center then the upper end is the same as the bottom except
only 2 seals

Take your flanged bushing on each end and bore them out a little over 3/4". That way they still hold your seals in but your driveshaft isn't making contact with the flanged bushing. They are getting hot because they don't have any grease getting to them. Even though they are oil impregnated, that's not enough once your driveshaft is turning 3,500 RPMs for any considerable time.

Just found out the bearings will continuously handle 250 degrees for long durations at 3600 rpm. Checked with a temp gun and not getting over 180. The shaft will handle way more, so we should be good. I mean, this design has been used for ages, guess I'm just overthinking everything.