4 Spd slight grinding when shifting.

Ok, I think I see whats going on.You have several problems.
-Problem#1)Lets start with the "stuck in reverse". As others have said, this is an adjustment issue.Since the tranny is on the bench, this is a great time to set it up. First we have to correctly install the cover. There are 3 types of bolts holding it on, and 2 types of holes that they have to go into,and 2 types of washers.First remove the bolt just to the right of the 1-2 lever.Im going to call that hole #1. Then remove any other bolt, except the 2 just under the 1-2 lever.If those 2 removed ones are the same, then theyre both wrong for that #1 location. That #1 location is special. If you were to remove the cover, and inspect all the threaded mounting holes you would find that the #1 hole is counterbored about 1/4inch.This is to receive a long-shouldered bolt, which will properly index the cover.So loosen all the cover bolts and go find the long-shouldered bolt by taking them out one by one.You should find three kinds of bolts; 2 plain bolts with threading right up to the hexhead,7 short-shouldered bolts and the 1 long-shouldered bolt.So assuming you found that bolt,Put it into the #1 location. The 2 plain HH bolts go just under the 1-2 lever, with plain spring washers.All the rest of the 8 bolts are supposed to have 1 size larger spring washers.They must all receive washers or they may not fully tighten up.The #1 also gets the little clip for the back-up switch wire.Dont tighten them yet.Screw the #1 bolt down to see if it will go in ok. Sometimes the shoulder-end gets mushroomed by novice installers putting it into the wrong location,and you will have to carefully smooth the end.So,once it goes all the way in,back it out a bit.Now with all the bolts a little loose, Push the cover up hard and tighten #1. Then tighten the rest.Ok the cover is on. But wait, what if the special #1 long-shouldered bolt is missing?Oh boy!Actually its not that big of a deal. The factory used a special procedure to select the reverse shift parts which required the #1 hole to be consistent.Since your tranny has a history of working ok, all you have to do is push up hard and tighten the bolt. Next,lets shift the reverse lever in and out several times.Put a 4 inch wrench on it.It should offer a small amount of resistance initially and then whack over easy,making a nice sound.In and out, whack-whack.If it doesnt do this and feels like its rubbing inside, you will have to do some adjusting.We will go there later, if needed.For now Im going to assume it shifts perfectly.So, reverse is done.Next,put that 4 inch wrench on the 1-2 lever and work it. You may have to line up the syncro slider by spinning the input shaft a bit.Shift; 1st, 2nd /whack-whack.Do this several times.Working good? Ok.Move the wrench back to the reverse location.Put your left hand on the 1-2 lever, then shift into reverse.Did you feel anything in your left hand? You shouldnt. Ok, back to neutral.Next shift the 3-4 lever. Shift 3rd,4th, In,out whack, whack. Finally put it in 2nd gear. Then try to also shift it into 4th. It should be impossible, with just a small bit of movement of the 3-4 lever. Ok cover is done.
---Problem#2)In my experience,these trannys do not like synthetics.Theyre just too slippery and will almost always grind shifts, especially neutral to first and the 1-2. I find the EP oils work, but the shifts are usually too slow for me. When the cones are fresh they will shift pretty good with Dextron II. As the cones glaze up and the brass wears they start to grind the 1-2 shift. The thin ATF also doesnt help to slow those big gears down,at all.So I usually run a blend 50% EP and 50% ATF. Works for me.So, if you dont know what oil is in it, just dump it.
---Problem#3)Shifter adjustment. You probably know how,so I wont go into it at this time. However, I will say this; Most of my shifter problems have been due to the levers coming loose on the studs. If theyve been run loose the slots get wrecked.So loosen the special nuts and inspect the levers for any for and aft movement.If you find ANY, you will need to fix it.I have used various methods over the years, usually expensive. Bot the easiest,simplest, least expensive, is Loctite RED.It needs to go ONLY 2 places;between the lever and the stud in the slotted index, and on the thread to nut interface.You must be very careful to not let any to travel up the lever into the cover.The slot area must be completely filled.After tightening the special nut,let it cure.
---Problem#4 ClutchPlate departure.This is checked with the tranny installed.I usually do this immediately after the tranny is snugged up to the bellhouse, and assumes all the pedal linkage is installed and adjusted.If you are experiencing grinding from neutral to first and you have no synthetic in the box, this is critical.Have a helper depress the clutch to the floor and hold it there.Now with a screwdriver you attempt to rotate the clutch disc.It should spin fairly easily.This tells us that the disc is in good shape and that the clutch fingers are all working and the hub is probably not bent.Next I install a couple of feeler guages about across from eachother or whatever you can get. I flip out the .040 fingers from the pack,and stick them in there with the rest of the pack hanging down.Then tell your helper to release the pedal.Next have your helper slowly depress the pedal again. Have him stop when the feelers fall out.If the pedal is not on the floor have him estimate the remaining travel,then release the pedal again.There is no benefit in over pedalling it, except maybe from neutral to first.If you have a diaphragm clutch, I would recomend to not overpedal it. Either lower the pedal by readjusting the freeplay, or put a block on the floor or under the pedal at the previously estimated height.Finally recheck the plate departure, and readjust as necessary.