FP sounds like the reel just doesn't step fast enough. Have you gone through and cleaned it? Springs nice and tight? Losing a point could be either that the next score comes in while the reel is still energized from the previous one (EOS too close), or that the pulse for the score is too short and the EOS isn't keeping the real energized long enough.

TA sounds like it's taking long enough to go from 9->0 that the next 1000s pulse comes in and manages to step the 10k a second time. 9->0 is always the hardest step as it has to move all those 9s+0s switches. Again, need to make sure it's nice and free, and springs strong. Can also help to lessen the tension of all the 9+0s switches (as long as they still close correctly). You definitely want the 9th position switch to open as soon as possible once the reel starts moving to minimize the time that another pulse can get through to the 10k

Testing good means nothing here, you know they work fine normally. It's a timing issue, as it only occurs when lots of stuff is happening, so just because the switch does open and shut doesn't mean it's opening and shutting fast enough and at the right times.

Also, at some point you're going to just have to accept losing points here and there. It's an EM, losing points is practically built into the rules (can't score 500 while score motor is running, etc). I'd be much more concerned with gaining extra 10ks than losing 100s