The 5400 has three independent movement mechanisms with three separate motors. I have marked the motors below:
No. 3 is the focus engine. It uses a gear train to move the film holder's carrier left and right. The gears are made out of plastic and are not very resistant. They may eventually break, and create trouble. But what you describe does not seem to be related to this mechanism.
No. 2 is the film holder's transport mechanism. It also uses a gear train to move the film holder itself left and right. The finicky plastic gears use in this gear train can also erode or break eventually. What you describe seems to have to do with these gears. It probably was not a good idea to force the film holder out. You probably damaged one or two of the gears by doing so, and although they work right now, they may give out under pressure.
The gear trains for the last two mechanisms are pretty simple and can be repaired with care if you have the spare parts.
No. 1 is the precision motor for scanning film transport, and is not to be messed with. The scanning transport mechanism uses a very robust drive shaft mechanism, and it is rather unlikely to break down unless under dire circumstances. It moves the whole film holder carrier back and forth.
I think all the three motors are stepper motors, although I might be wrong.
Below is the gear train for film holder transport:
This is located right behind Motor No. 2. It consists of one metal gear on the engine shaft itself, and a gear train including four plastic gears. Unfortunately I don't have a picture with all the four gears, but you see the naked shafts for Gear 3 and Gear 4 here instead.
Gear 4 engages directly with the cavities that you can see on the bottom surface of your film holders. It is actually the pinion for the rack and pinion mechanism that drives the holder back and forth (film holder is the rack). This gear is made from a material harder than the others and yet it is the one that often gets damaged.
I had similar issues with the holder transport mechanism, and finally last night I could change the damaged gear with one that I salvaged from a broken 5400. It was a rather easy fix, but I know it won't last forever. I am also thinking maybe we can 3D-print or cast this piece. I am sure there are plenty of 5400s lying around with that gear broken.
If I were you I would keep my eyes open for a broken 5400 on the eBay to use for spare parts, just in case. I actually got mine here, from a mate who was kind enough to send me his broken scanner.
Hope that helps.