t 90 issue post motor swap

I recently had a 196 swapped into my s80 to replace my 152 and have run into three problems. Would be interested in what I can do to troubleshoot, or any recommendations from the community.
1. On a limited test drive, I got a strange noise - a knocking sound that I can feel through the transmission by gripping the t-90's shifter. On a limited test drive this seemed to pop up after cornering (strange I know), and barely when accelerating. Sometimes it is smooth and there is no issue, other times it is significant. This one has me baffled!

Issue with the noise under power after the engine swap has gotten worse. Newly rebuilt tranmsission, transfercase, and drive shafts prior to the rebuilt and it shifted ran perfectly. After the engine swap, once it is in gear there is a loud chirping chattering sound in every gear. It goes away when I push the clutch in. It shifts smoothly into gear.

Help from the experts: what do you think it is, what should I do to fix/troubleshoot?
 
A chirping sound usually indicates dry "cracked" steel against steel. Or cracked steel moving back n forth rubbing against it self. " for instance, an example: a cracked flex-plate on a automatic will chirp if it's cracked." could be a possibly failed bearing ? No lubrication.? Can actually be a number of thing's. Jeff
 
That's a big ? Did you rebuild the trans or get it that way ? On the front input shaft of the tranny,is a little hole that lubes the front input shaft bearing,if for some reason,they siliconed the front retainer/housing on,if they didn't have a gasket,it could have got in that little hole ,is 1 thing that comes to mine.? Boy man,there's so many possibility's here. Pull the tunnel cover off,an pull the top off the tranny an have a look see,that'd be the easiest for starters.Jeff
 
You have two issues that need to be addressed. Both of which we have discussed when you came to pick up your Scout. Which I'm sure has not been taken care of. First, your carb needs more fine tuning. I didn't mess with it much mainly due to the fact with all your talk of swaping it out for a different type of carb. And second, your ignition needs to be fixed. I had mentioned to you at least twice that your ballast resistor needs to be replaced, due to the fact it is/was broken. I had, also, suggested upgrading to pertronix in you distributor. Which is on sale right now untill March 31st through IHPA. By doing so, will able you to eliminate that ballist resistor altogether. Both these issues, carb and ignition, will only help your motor to run better.

Other than that, it's kind of a guessing game and shooting in the dark in trying to solve what you hear. When I test drove your Scout after I did the motor swap, I didn't hear what you seem to be getting.

Btw - I have been aware of those dowel pins that locate the transmission bell housing to the block probably longer than ya been alive. And yes they were in place when I put the newer used motor in.
 
Update:

I started the engine while the Scout was in neutral, and there was no knocking sound or chirping sound. After it warmed up there was a knocking sound that speed up as I increased the engine rpm's, and decreased as I slowed the engine rpm's. As soon as I pushed the clutch in, the knocking sound went away, and as soon as I released the clutch the sound came back.

Does this help troubleshoot where I should look?
 
Was a lot of stress put on the input shaft during disassembly or reassembly. If so the bearing on the input shaft or the pilot bearing on the main shaft could have been damaged.
 
You called it right...

I opened up the transmission and everything looked perfect, shiny, and new. No teeth missing, chipped, or cracked (see attached pic).

Took a second look and noticed that the front imput bearing is thrashed (see attached pic).

So it looks like in addition to the motor swap I'm going to need to do something about the transmission. Do I rebuild the t-90 for cheap ($400) or invest in finding and then installing a 4 speed with the pancake bellhousing installed? Tough call since I can't do the fab work for the 4 speed - but can do the t-90 install.

To be continued...
 

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