So the EOS checks fine in switch test? Remember changing everything doesn;t make a switch work, and it can screw it up. Go in test and make sure the EOS is registering....

You have a lot of possibilities here.
Switch work?
Follow those wires back are they shorted on the way back to...guessing it's a fliptronic board in the head?
Those fuses are fine?

After all tat comes the next step. I don;t know it because I have a machine that has had that error for a couple years and I just ignore it

Are the EOS switches new? Are they properly gapped? Did this problem happen as soon as you rebuilt the flippers?

So many questions!

It appears that ToM has a Fliptronics board for the flippers. According to Clay's guide, it looks like games that have a Fliptronics board should have the EOS switches gapped normally open (meaning they should close when the flipper is activated). Check the left flippers EOS switch. Is it gapped properly?

I doubt there's any correlation there, but i could wrong. Researching the problem a bit more, it looks like it would be worth taking a close look at the wiring to the EOS switches (both). Apparently it's not uncommon for a wire to break off one of the switches solder lugs. Gently pull on each wire going to them to be sure the wiring is firmly attached. I would also clean the switches by swiping a business card or folded up piece of paper between the contacts a couple times to be sure they're making good contact.

According to the manual, looks like that black/blue wire should be going to pin 3.

Screenshot_20180415-141631.png

I have an Indiana Jones: The Pinball Adventure. I know the OP started this on another game , but I am having a problem in exact the same are, be it a different problem, so I hope you dont me asking a few questions here
- Problem : Left flipper EOS switch does not register. It always registers as open.
- I cleaned the contacts with a business card but this did not help
- in switch testing mode shorted both leaves (by pushing them together and by holding a screwdriver against both leaves (just on the spring metal)) and this does not register, if I do the same on the right hand side it does register
- then i measured the voltage over both leaves and on the wires on the switch: the non-working left flipper EOS switch registers 0V the right EOS switch 12V
- Found in the manual that I should find J906-3 for the blue wire, which is there and the orange wire on 6. Found the connector and disconnected it but saw nothing obviously wrong with it.

Now just wondering if I have my next options correct or maybe some tips:
1) Most logical thing seems for me to disconnect the connector and test voltage difference between pin 906-3 and 906-6 on the connector on the board to see if I see a 12V difference on my Analogue Multimeter (DMM on order ). I am just afraid that I hit one the other pins while doing this and short something. Especially as the fliptronic board is in the top left corner which is kind of hard to reach .
2) The other option would be to check continuity on the two wires, between the disconnected connector of the fliptronic board and the solder points on the LF EOS switch. Problem is that connector pins are tiny and I am struggling getting in with my MM and it is kind of an awkward reach between two connectors.
3) another thing I was thinking is to check the voltage between LF EOS ground and RF EOS + to see if I see a voltage difference, if not between LF EOS + and RF EOS ground to determine which of the two LF EOS wires are not supplying the right voltage?

Any suggestions on my thinking on 1, 2 or 3?

Disclaimer: I literally started on my first pinball machine a few weeks ago and am self teaching and enjoying myself. I do try to look up stuff in the manual, this great forum and youtube, and am surprised how much I can find but sometimes I just think: there should be a better way : so really sorry if these are uninformed questions.