Wow, thank you for the detailed explanation. I had this here so I thought I would just re-pin the original harness to neaten things up a bit, but maybe the modern switcher/re-pinned harness is the way to go.
If by re-pinning the original harness you mean restoring it back to unhacked status by installing the original type of Molex connectors onto the cut wires, then, about 6 months ago MikesArcade started selling the exact same type of adapter harness that I made about a year ago, and his appears to include a power supply:
https://www.mikesarcade.com/cgi-bin/store.pl?sku=PSK-PP-1000A
If you already have a modern switcher he would probably sell you just the harness by itself, or, you can easily make one yourself like I did. Use 18-gauge stranded hook-up wire (100% copper).
For the connectors you need:
(1) Molex 5025-series 9-position housing (part number: 15-31-1091)
(1) Molex 5025-series 12-position housing (part number: 15-31-1121)
(11) Molex 5006-series male terminals (part number: 08-70-0043)
(1) Molex 3191 series 3-position housing (part number: 19-09-2038)
(2) Molex 1190-series male terminals (part number: 02-09-2103)
The pinout is like this:
That view is from the back side of the housings (the side that you insert the pinned wires into). The 3-position connector, which is for the 100 VAC input from the stepdown transformer, just uses two wires with the middle position being unpopulated (which you can see in the picture of the harness I made). It doesn't matter which wire goes in which position because it is AC.
Also, ignore the +24v connection; that's only for the coin meter and standard switchers don't provide +24v.
If your Punch-Out cabinet's harness is missing its three Molex connectors that plugged into the original power supply, to replace them just order the terminals and housings that mate with the ones I listed above. That will allow you to plug directly into an original PP-1000A power supply if you ever decide to.
On the Punch-Out harness' edge connector, pins 11-14 are for ground and pins 15-18 are for +5v. Pin 23 is for +24v if you want to populate that for the coin meter (only relevant if you ever decide to use an original PP-1000A power supply).
As a side note, on an original unhacked harness, more positions of the 12- and 9-position connectors were populated than are necessary. With the 9-position connector, every position is populated, but the mating connector on the original power supply only has 6 positions populated. With the 12-position connector, 10 positions are populated while the mating connector on the power supply only has 6 positions populated. I have no idea why they did that, but it obviously isn't necessary to replicate those dead-end connections when putting new connectors on your original harness.