Very rough engagement after manual tranny swap
 

I just finished swapping a R150f into my '91 V6 4Runner after the auto bit the dust. It is a rebuilt tranny from Marlin, and the following things were also included in the swap: ceramic heavy duty clutch and 1600 lb. pressure plate, new flywheel, stock chain t-case, manual tranny computer. The neutral start wires were crossed for now until I get the clutch start switch all wired. This should mean the computer thinks it is in neutral all the time.

Everything in the swap went fine except for the fact that I need to just get the heavy duty organic fiber clutch instead of this ceramic clutch. There is no slipping this clutch, so city driving is not pleasant at all.

The main problem I am having is when I am coasting all gears. I will be in say 4th gear trying to keep a constant gas pedal pressure (not speeding up or slowing down) and if I barely let off, I can feel a big drop in rpms and almost like the tranny is disengaged from the engine. Then, I can press on the gas a little to get it "engaged" again, and it will hesitate a little until there is a pretty harsh clunk and then it starts to accelerate again.

This happens in all gears (the sudden "disengagement" and "reengagement") and it's just really annoying, and I know it will take a toll on the rear end and new tranny. The engine has missed and hesistated a little for a while, so maybe the combo of the new manual tranny, ceramic clutch, and possible need of new plugs, wires, etc. makes it all worse.

Sorry this is so long and difficult to explain, but hopefully someone has had the same symptoms and maybe an idea of what I should look at.

Did you?
 

I just did the swap myself. Did you replace the driveshaft with one from a 5-speed 4runner? If you just overextended the auto driveshaft, you may have some binding which could be the cause of the "clunk". On a side note, have you figured out the ADD wiring? I do not know which wires to splice into.

No I had the driveshaft lengthened and added a CV joint at the t-case end when I did the lift initially. The yokes are getting close to coming apart, but it is still a solid fit with little play. I am going to have it lengthened again soon, but I don't really think that is the problem. It just feels like something is unloading and them reengaging when I let off and then get back on the pedal.

Your angle of the driveshaft probably changed since there's a length difference in the transmission/transfer case. Your CV joints on the shaft are sittling at a different position than they were before. I think it will go away over tiime. Lenghtening the d-shaft again help.
When I did my SAS, I took a pre 86 front d-shaft and lenghten it.