Welcome to the technical world of EM's - Once you solve this problem you will breeze through any problems with the Capt Fantastic.
Unfortunately if there is 1 wire off or a dirty/open or closed switch in the start up sequence it wont operate fully.
Is there any scoring at all when activating slings/drop targets etc ?
Suggest you put it on freeplay http://www.pinrepair.com/em/index3.htm#free & follow the startup sequence http://www.pinballaustralia.com/startupW.htm
Keep the updates coming