Hi,
First be careful with the "bag of parts" as the M46 can have two different clutch kits.
In 1978 forward the splines on the input shaft changed in the numbers of! So consequently, there are two different friction discs in very similar kits. Do your research and see what the 1982 uses.
By 1989 or the introduction M47 series, of which might have been a little earlier, the flywheel change in depth for a shorter easier working clutch pedal. So that requires a different clutch kit altogether different.
The flywheel turning is optional in most cases except for excessive grooving from disc rivets and any kind of discoloration or hot spots.
Inspect the old pressure plate for this too. Not that you are going to do anything else with it, but for heating signs as the flywheel took a beating if it did.
I run an dial indicator on it to check for run out. If there are grooves to affect the reading I suggest getting it ground flat or at least give it a coarse sanding. This is same way I do brake discs and for the same reasons. To clean off friction material residue, but I run the engine to spin it.
Pilot bearings are removed with some grease packing done behind it and a round closely fitting shaft pounded in through the middle of the center diameter.
A alignment tool is used for the disc centering. It aligns itself into the pilot bearing that you will replace and should be in your kit along with the throw-out bearing.
The tool holds the disc as you bolt down the clutch plate housing to the flywheel.
If you are going to change this out just above a floor or garage apron make sure you get the car up as far as you can and of course very stable.
The best would be to have the bottom up to around 18 inches high on heavy duty floor stands. You are doing more than a tire change or an oil change.
The more the better because as you moved the transmission back you will need to rotate the whole unit counter-clockwise or tilt it over.
With this on a jack or rollers it's pretty thick.
You need to get the starter hump on the bell housing lower and out of the way of the fire wall.
It needs to move back at least four inches to clear the pressure plate housing.
The transmission jack (best) or a regular floor jack will have to hold the transmissions weight up from front to rear and with straight back movement to clear the input shaft out of the clutch.
This thing is not as heavy as an automatic but it's heavier than the M47, that I can carry around fairly easy. The cast iron and the overdrive unit put the weight in the middle of both.
A hard to shift transmission can be that way if the clutch disc is sticking on the splines of the input shaft or not sliding per say. The disc needs to float between the flywheel and the pressure plate.
In this case, you should be having trouble with getting into reverse as well.
If you are not having an issue with it towards reverse, then you might have other issues inside the transmission.
These start with the synchro's or bearings you are hearing on the third and fourth gears.
One has to keep the shafts aligned radially and the thrust clearances laterally between the gear faces and synchro packs.
A fresh oil change of ATF Type " F" fluid is a must to make a fair diagnosis of shifting.
No telling what lurking around in between all those precision parts in there.
There is not a lot to do to the overdrive if it's shifting good. There are two filter screens you can clean but that will not cure any other issues you mentioned. Besides filters are done from the outside under a rear excess plate.
The oil needs to be changed every 30,000 miles or less without fail during its lifetime.
Do you know any history of this happening, at any time, by you or service records?
Since you are in for a clutch, you had better do a flush and rinse with some cheap solvent like kerosene for a massive rinsing. I say save a better solvent for a final rinse
Pour it down through the top of the gear box and out the bottom. Inspect the fluid for metal flakes.
Blow as much compressed air in as you can around to help dry it out.
A truely more evaporative solvent, comes in handy here, for a finale of all your efforts.
Inspect the synchro's teeth for excessive wearing, if you saw some bronze come out.
Ragged or rounded edges on the angles and shiny patterns that are uneven are not good.
If you can find a specification for end clearance between the gears using a feeler gage might help you locate thrust issues.
Radial play is a bit tougher, but if you can shake a shaft or a rotating member, you could have bearing issues. Rotational noise or roughness in turning shafts, well that, says your done!
A rebuild is in a coming order.
If you don't see something obvious then put it back in and go with it just to see if that helped or made it worse.
Keep us in the loops if you run into snags!
Phil
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