Transmission woes - what's wrong?

[jt15833]

Just recently got my 240 on the road after a longggg downtime. I had a CA18 in it and then I sourced a KA24DE engine and transmission from a shop. Long story short I got it running good and took if for it's maiden voyage just these past few days.

First, the engine runs great. Strong, no leaks etc. My issue is with the transmission. If I am idle w/ clutch in, I can shift through the gears without problem. The problem is however, that sometimes, when I let the clutch out, in 1st for example, I hear a really grindy/rough noise from the trans. that varies as the clutch comes out then it's all the way out and I'm moving. Then if I am moving and shift to 2nd I will usually hear roughness again and experience the clutch-out experience again.

The clutch out experience is a little different for all gears, for example 2nd is pretty rough while 4th isnt too bad. It happens probably 60-80% of the time, and when it does, it's always the same (for each gear).

Also sometimes when coming to a stop with the clutch pushed in, the transmission will make the same rough noises until I pull it out of gear. During all these occurrences I can feel a lot of resistance and feedback through the shifter (isis short shifter).

- Things I've though could be the problem;
1. obviously the transmission. I think this is the source.
2. I am thinking though my clutch could use adjusting. I have bled it to the best of my ability, from the slave cylinder. I removed the other line behind that and I don't think I have another bleed point. Perhaps I can adjust the pushrod near the clutch pedal?
3. After looking through the FSM I realize I am missing the ball and spring that goes into the transmission near the shifter plate, it gets inserted at the same place/direction as the screws that hold down the shifter plate. What is this?

Thanks guys, I'm pretty sure it's my transmission I just want to learn about my problem.