Your problem is your too gung ho, fixing a game properly takes lots of work and time...just because you have a new power board, doesn't fix the original problem that took out the old one. You can't just hook everything back up and expect it to magically work. You need to be able to be Sherlock Holmes and find the start of the problem, fix that, then repair the damage to all the other areas that first problem started. Most big problems on pinballs is that someone tried fixing a small problem, didn't have a clue on what to repair, then started doing more damage, and gave up, passing the game/trouble to someone else, they did more damage, and now you have the game, and your trying to repair all these items at once. Sounds like the cpu board has a few driving transistors blown and possibly the predrivers/resistors. You might also have pinched wiring between the head and cabinet, and a wire touching ground. There is a grounding braid that goes all around the inside of the game, everything metal is attached to it in the cabinet and head, (not the playfield), such as transformer, rails, coin door, speakers, and the metal plate holding the boards in the head.
The coils have positive power on at all times, the computer completes the circuit by closing the ground circuit, making the coil fire. If any wire is loose or damaged, and it touches an object that has been grounded by the braid, it can do damage to the game. Check all wires.
Pull out your large cpu board, lay it flat on a non metal surface. Using your tester, set it on beep test, ground one wire to the boards ground, and using the other lead test. Tap the top of each of the driving transistors that are located along the bottom of the board. If you get a beep, it's bad. Inspect its predriver and resistor for damage also.
Here's a few pix to go by. 16 transistors in lower left, 6 in upper right for the coils, leave the lower right alone, those are for lamps. You'll notice what a blown transistor might look like, a burned resistor and the predriver Q72 in the middle, all bad. GL