You can also use these test ROMs to help you diagnose along the way: http://pincoder.ca You will need at least one 2532 or 2732 chip and a programmer to use them.
Try the suggestions in the guide that frunch suggested. It will get you familiar with your game and hopefully fix a few things along the way.
If things still don't work after that try the pincoder ROMs. The main purpose of the ROMs is to allow you to isolate and test independent circuits so you can troubleshoot one thing at a time. In fact, I created the system 7 version using a Black Knight that was in really rough shape and now it runs like a top!
There's a pinside thread if you have any questions about using them too: https://pinside.com/pinball/forum/topic/new-williams-system-6-in-game-test-roms/page/4#post-4996073