Transmission Help!!

Hello, I was having a problem with my starter. I was getting nothing but clicks when trying to start. Tapping the starter seemed to allow it to crank, so I made due for a while. However last week the check engine light popped up. Now the car will not shift from 2nd to 3rd. I can manually shift from 1st to 2nd then nothing.  When I start out in drive it seems like it starts in second and will not shift at all. Transmission fluid was really dark had to drive 30mph to advanced to get a new starter,  filter, and fluid ATF+4. Had a kid run a hand held diagnostic and nothing popped on the trans. Then for some reason on the way home the car drove fine and shifted perfectly. Next morning same problem as before, check engine light still on. So I put on the new starter and replaced the tranny filter and fluid. Starting issues are solved, I let the car idle for 15-20 minutes and got the fluid levels up to par. I had to Add 7 quarts then took it for a test drive and all seemed well. Then this morning it was back to doing the same thing. So my question is could I have knocked something loose banging on the starter. For instance the linkage that runs along side of it. I was told it could be a shift sensor or solenoid. Are there any simple solutions or adjustments I can try?