I did something similar on my ST:TNG and it was a beast to fix. I took out the CPU board to fix another machine, and when I reinstalled I plugged one of the ribbon cables in backwards which fried a bunch of stuff. I would recommend the following.
1. If you have a photo of the open backbox before your switch, make sure everything is plugged in the exact same way... I did not catch my error until I carefully compared photos looking at bends in the wire. If you don't have a before photo, look at other people's for sale photos until you find a good one.
2. Assuming you do not identify the error in step one, remove every fuse, even the ones you think look good and check with a multimeter, you may find another bad one.
3. Check blinking light logic on CPUs board on page 1-39 of manual... based on your description this will most likely have isseus.
4. If fuse 104/105 are blowing, find the associated circuitry in the manual and unplug the relevant cables on the power driver board. Page 1-39 of the manual says the 104/105 are Solenoids 1-8 and 9-16.
5. Page 2-48 of the manual says the associated backbox plugs for these solenoids are 126, 127, and 130.
6. After you have verified all other fuses are good, try restarting with 126, 127, and 130 unplugged, if the fuses still blow your issue is on the board somewhere.
7. If they don't blow, plug them in one at a time and power cycle to see if they blow, and use page 2-48 of the manual to diagnose relevant parts to check.
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