Motorcycle Repair: Transmission wont shift, while running, clutch lever, dry clutch

Question
QUESTION: Shift problem led me to install new trans.  Now, trans shifts easily, until motor is running.  When running, I can get into 1st, but only can up/down shift if I rev up the R's.  Please help.  Also, adjuster screw w/jam nut on the side, what's it for?

Thank you

ANSWER: What year and model?
Mike

---------- FOLLOW-UP ----------

QUESTION: Custom.  Using a Harley stock 80ci, BDL 3" open primary, aftermarket 5-speed.  The original 6-speed chewed up the throwout bearing, melted the pushrod, and ground the clutch adjuster into a mushroom.  I replaced the bearing, and the pushrod.  I replaced the rod and bearing, but still had shift problems.  That led to the replacement 5-speed.  Will be ordering a new adjuster, rod, and bearing today, just to try.  I'm sure I did something to tear up the old stuff, but with a new trans, the only thing I reused, was the clutch adjuster.  The bike doesn't "walk" when running, so I don't think the clutch is dragging, and there's plenty of play in the lever.  I'm a troubleshooter in another field, but I'm stumped.  Don't understand why the bike will shift when off, and not while running.

ANSWER: Remove the derby cover. When you pull the clutch lever do you see the clutch plates moving? How much play do you have in the clutch lever?
Mike

---------- FOLLOW-UP ----------

QUESTION: I have an open/dry clutch, and yes, the plates move.  There is between 1/4" and 1/2" play, right now.  Once everything is running smoothly, I intend to adjust the play to about 1/4".  The bike does not move while running, in gear, and clutch pulled in. Doesn't seem like the clutch is dragging.

Answer
You should have about 1/8 inch play in the clutch lever. When you try to shift it while running, does the shift lever not move or is binding like it does not want to go into gear? If that is the case, then is sounds like the clutch is not disengaging. remove the adjustment you have in the clutch lever and put alot of slack in the cable. Now go to the adjuster on the clutch and turn it outward a few turns. turn it back in, just until it bottom out and then back out about 1/8 of a turn. then adjust he cable like I said above. let me know if this works
Good luck and happy riding
Mike