Regarding your alligator clip leads, pull back the rubber sheathing and check that the wire is actually soldered properly to the clip, often they are soldered poorly.
Check the rear side of the solenoid driver board.
Look for dry solder joins on the header pins. You are looking for a 'crack/s' in a circular area in the solder where the pin/s comes through the board.
Check the plugs themselves, J1 & J2. A pin could be broken or have poor connection.
I read you are going the simple way first, but IMO those flipper EOS switches should be replaced.
Start a game and using your multi meter put the black lead on any metal part of the body, that being the ground, and then put the red lead of your multi meter on the coloured wire of the LH coil being Green, you should get a reading of about 43VDC.
You can check using the same method on your working RH coil, but put your red probe on the Orange wire.
You will notice the flipper coils, LH & RH have a common coloured wire, being Brown, this is power from the Rectifier Board, the other coloured wires on the coils are from the solenoid driver board.
The wires go from the cabinet to the bottom header/plug of the solenoid driver board, J2 then out through J1 on the solenoid driver board to the playfield.
The relay is in the middle so to speak.
With the flipper enable relay 'ON' one part of the circuit is complete, the other part of the circuit is 'closing' the flipper contacts in the cabinet which provides a path to ground.
I get being new to this it can all be a bit daunting, hang in there, you will sort it out.
Also, IMO paper/cardboard is only good for cleaning gold plated contacts, you should really use at least some sandpaper, if not a nail file/points file or similar to clean tungsten tipped contacts.
And the normally closed (NC) EOS switches with the tungsten contacts need to make very good contact, meaning zero ohms resistance between/across them.