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I could really use some advice. I bought this truck 3 weeks ago with the engine out of it. I attempted to install it but it just wouldn't line up on the bell housing. I pulled it again and this time I put in a new clutch kit hoping the pilot bearing was the issue. 3 hrs later last night and I have the left side mating but the right side is a half inch out and doesn't want to come together. is there a trick to this or something I'm missing.
Make sure your clutch plate is centred properly first. Try supporting both the engine and the gearbox with jacks and slowly raise and lower them to bring them into alignment with each other. This happens a lot and you need to get the engine to butt up to the transmission bell housing evenly or it will bind up on the bolts. This could damage the clutch plate centre and/ or the input shaft trying to force them together.
be sure the input shaft tip is absolutely clean, or the tranny will not bottom out. Found that out the hard way when I put in a jy tranny that the tip was rusty, and it only went partway in, and when we tried to pull the tranny out, it pulled the pilot bearing out of the flywheel, and we had to unbolt the pressure plate through the bottom gap of the transmission to be able to get the bearing off the shaft. Not fun!