Sounds like you could have problems with the solenoid driver board 5v jumper. Check the jumper on J3 pins 13-25 of the solenoid driver and make sure its not loose. Remove the board and resolder the pins on J3 and around the flipper relay.

The flipper is a stand alone circuit from the rest of the game. Since the flipper problem started after you rebuilt it you should start there. Check the adjustment of the EOS. You should be setting the EOS by pressing in on the plunger with your finger and not turning the flipper. The EOS is normally closed and should open at about 80% of the flip stroke. Also the left flipper is s double flipper switch. The EOSs should be adjusted so it's 'break-make' with the upper flipper.
If this all checks out look over the SD board as I describe above. You have a flaky connection in the flipper circuit.

You do sound a bit lost. Lets simplify this. You say the right flipper fires once and stops. That sounds easy to troubleshoot. First step is to make sure there is 43v on the flipper coil. That's an unfused solid brown wire.
Get the game in mode where the flipper is not firing. Check for 43v at the flipper. If it's there pressing the flipper button should send a ground to the other side of the coil. Lets figure out why the ground is not getting there.
You need a ground test wire. The frame of the game will work for that. Temporarily connect a test wire to any convenient ground like the frame or ground braid. Momentarily shorting that ground wire to the flipper wire should make it fire.
Now, how does ground get to the flipper to make it fire? Ground leaves the rectifier board at J2-2 and travels to each flipper switch. It leaves the right flipper switch and arrives at the SD board at j2-1, travels through the relay and departs the SD board for the playfield at J1-8.
What you need to do is short ground to each of those points until you find a wire that shorting ground to will not make the flipper fire. I'm thinking along the way we'll find a bad connection also affecting the coils.