I haven't tested this thoroughly.
To reverse the gate coil software logic:

Open the U1 ROM in a hex editor and change:
$0000: $EC ---> $F0
$02A1: $9A ---> $96

Open the U2 ROM in a hex editor and change:
$011D: $CE ---> $D2
$031F: $9A ---> $96
$0789: $96 ---> $9A
$07DA: $96 ---> $9A
$07ED: $90 ---> $88

Note: since you reverse the mechanical logic, the gate will now be normally closed instead of normally open in attract mode (in order to keep the coil off).

Location $0000 is the checksum for the lower half of U1.
Location $011D is the checksum for the lower half of U2.
Location $07ED is the checksum for the upper half of U2.

If you look at the values changed, the math is pretty straight forward. The checksums have been accounted for. It boots fine here.
Suggest trying the modified/combined U1+U2 with the factory U6 code. Take Olivers U6 code out of the equation for the moment.

If it still doesn't work, please post a file comparison of the original combined U1/U2 vs the modified combined U1/U2. From a command prompt:

fc /b combinedU2.org combinedU2.mod

combinedU2.org = combined U1+U2 of the original code file
combinedU2.mod = combined U1+U2 of the modified code file

The values changed from 9A to 96 simply change the call location from coil off to coil on for the gate, and vice versa from 96 to 9A.

It sounds like you've got an interrupt problem with the board now..

Is the MPU LED going dim after the 7th flash or is it switching off completely?
What do you mean by "activates all the coils"? When exactly is this happening and are any locking on?

The moment you power on you should see the LED very quickly flicker. Don't count this. This flicker just says the CPU has started booting from the U6 ROM.
Half a second later you should see it flash then extinguish, this tells you the ROMs have passed checksum test.
There will be a bit of a pause as the game tests the volatile RAM at U7. On success it will flash and then flash another 5 times as other board components are tested. There are 7 flashes in total, not counting the initial quick poweron flicker.
After the 7th flash the game enables interrupts and jumps to the U2 ROM to initialise the game and run attract mode. And the LED will stay on dimly which tells you it's processing the display update interrupt service as it should.

I burnt the doubled U6 and modified combined U1+U2 here into 2732's and put them onto my old different Bally with the solenoids disconnected. The game boots and runs attract mode no problem (wrong lamp sequence of course). And I can start a game.

Somethings wrong/corrupted with your U2.

Dump the ROM and compare it to the modified source you programmed it with.

If you've ever played Black Hole, you'll know all about this interesting challenge

Just as a test, where the middle post is under the right slingshot, if you lower the rubber at it to reduce the lane gap, there might be less chance of the ball bouncing up into the gate where it can be forced open. Maybe try temporarily stuffing something at the post to see if it makes any difference.

HarlemGlobeTrotters_Inlane-mod (resized).jpg
HarlemGlobeTrotters_Inlane-unmod.jpg