OK MSF uses a direct and solid state control so kind of a hybrid. Definitely do what TDA suggests and check your cabinet fliper switches. They are the direct power control and are tungsten contacts. They do need to be filed once in a blue moon and need to close tightly and squarely to conduct full current. By your description this sounds like the most likley cause of your problem. However...
The other end of that is the end of stroke or EOS switch circuit which needs to be CLOSED at rest and open about 1/16" to 1/8" at full flipper stroke. The points need to be tight when closed and clean. Do not file these, however as they are gold plated, not tungsten. They do not conduct high current but do tell the solid state fliper board to keep pulsing high power until they are open at the end of stroke.
Lastly, for now, check the fuse clips! DE/Sega was known for having cheap, weak fuse clips and without enough tension holding the fuses in the current just can't get through. Trust me, they may look just dandy but pull the hig power fuses and try to wiggle and squeeze the clips. I had one game where 6 clips fell off in my hands when pulling the fuses! Notoriously bad.