I can't believe this hasn't been mentioned yet- If your machine does not have it.
#1 mod- Drac Track support bracket that goes underneath to keep wear from appearing on the play field. Here are directions on how to install and check to see if you have it: http://www.marcospecialties.com/pinball-parts/01-15202
After that
Mantis scoop protector as mentioned earlier as the Mosh Pit can become the size of an orange if not protected. If wear has started, then a Cliffy. (Some use the Cliffy instead of Mantis your choice.)
LED under the inserts. This game has a lot of inserts and it is hard to see what is lit with incandescent lights. Frankie's head is a good example.
If you are going to put new decals on, get the metal standoffs so the legs don't wrinkle.
I have Z doors painted figures and they are awesome. A million times better than the originals and pictures do not do them justice.