Hi, I’m Chris. Welcome and thanks for asking your question!
You stated the trans was rebuilt then mentioned all new clutch components, did they actually go into the trans with new parts or did they just address the clutch components?
Is this only a concern while not moving, or is it an issue while driving and rolling?
The receipt I have shows a complete rebuild kit installed in the transmission in addition to clutch work. Problem shifting is while engine is running or car moving. Also hard to shift into 1st or 2nd if I have engine running and leave in neutral with clutch out then try to shift to 1st or 2d. No problem when shifting to any gear with engine off.
Just so I understand sitting still with the engine off, the shifter feels fine and can go in and out of 1st and 2nd trouble free?
Sitting still with the engine running it is hard to get in and out of 1st and 2nd and the shifter feels harsh or binding?
Engine off- no problem shifting. Sitting still with engine running and in neutral with clutch out, hard to shift when I push clutch in and try to put in 1st or 2d. Sitting still If I keep the clutch pushed in and do not put it in neutral, I can usually also shift with no problem. Don't know if this answers your question.
Yes that does help.
I am not yet convinced there is an issue inside the transmission with the 1st and 2nd synchronizer or shift fork or fork bar and shifter rail linkage. I believe the concern is the input shaft is still turning when you press the clutch in. If you feel like the clutch pedal and distance feels like it should then I blame fault on the parts used in the bellhousing. The pressure plate or clutch disc are not the correct thickness, most likely from being aftermarket. Normally this is a result of a clutch disc being to thin or a pressure plate with weak steel used that is flexing and not transferring movement when the slave cylinder is pressing on the fingers to release the spring tension on the pressure plate and allow the clutch disc to come to a stop.
What you can do is park on flat concrete. With the engine running and shifter in neutral. press the clutch in and slowly try to push the shifter in 1st gear. If the vehicle makes any attempt to move forward. Then the clutch is still engaged partially and spinning when it should not be. This means the transmission needs to be removed so the clutch can be repaired again. This time I suggest motorcraft parts be used including the pilot bearing, clutch, pressure plate, and slave cylinder and have the flywheel machined if there are any hot spots.