In order of hard to do in my opinion...

-I would definitely completely replace everything on the jet bumpers but the metal bracket, plunger and caps while the playfield is out. They are harder to rebuild in the game since they are so far back.
-Decide if you want to add the pop bumper area mylar while doing the swap.
-Replace every switch that has given you a problem ever
-Rebuild the flippers completely while out
-Clean check the up/down bank, rebuild drop target bank and diverter
-Rebuild all solenoid mechanisms at least with new coil tubing and evaluate the coil stops
-If you are into LEDs this is the time to do it.
-Check the playfield hinges, now is the time if they give you trouble
-Now is a good time to replace the coil wrappers if you care
-New rubber
-New plastics if you want them
-Replace the GI plugs while out if they need it. AFM was early WPC-95 and the driver board tended to burn these.
-You should check for broken ramps once they are out especially the center ramp. But the game is easy to shop so no big deal doing this later
-I always have had to replace a few plastics posts on playfield swaps. Check for short vs long red skinny posts as you remove them. I think this game has both sizes
-I remove and clean the 3 harness’ also but that depends on your comfort level
-I have had replacement green targets break pretty quickly on either side of the saucer so I would keep the originals if they are ok.

Have fun

If you look in the manual on page 2-39 I think what you are talking about is number 28. I found it at Marco or Bay Area. If you still have the ball trap standoff along the left wireform by the popper (number 20 I believe) that is what was in my game when I bought it. So a standard 2" would probably work if you can't find one.

Yes on the jumpers instead of diodes, Clay had a guide to do this so pinwiki probably has a picture.

Those GI connectors are pretty typical. Get the .156 connectors and pins from Ed at GPE. the housing are the same but there are different pins for 20-22 AWG and 18 AWG iirc so shoot him an email asking for what he recommends. I think you should replace the header pins also if they are burned. I had to that also to get my GI working again.

I also forgot to suggest the mini-saucer mod while swapping the playfield. It is ahead of the colordmd in my book.