I started by removing / rechecking the 2 transformers for jumper blocks for power output ranges. There was none found on ether one of them. So I guess this cant be changed.
It's not a jumper block. On the transformer from my MK2, Midway brought all the input taps out to the AC input connector. Looks like the same situation here from the picture. The other side (cabinet side) is then jumpered to wire things up as desired for local line voltage. However, it sounds like something on the output of the transformer may be shorted from your description below.
I decided to take the AC wires coming from the AC line filter (coming from the wall) and connect them directly to the input on the main ISO transformer. Thus by-passing / eliminating the wiring that goes to 4 prong toggle switch, then threw the 3 cherry kill switches. This made the transformer make a sound that I had not heard before... It sounded like it was powering up !
Transformers in general should not make noise other than a very light 60Hz (or 50Hz in Europe) hum. If it sounds like a bunch of rocks in a tumbler, then either something is broken (and this can sometimes be fixed) or the secondary has a short somewhere (either in the winding itself or one of the loads).
I took some voltages on the out put / isolated side and saw that it was giving 170v AC. That’s better but still not good.... So I then decided to put the black ISO transformer back in and plugged it into the wall (remember it gives 80v AC). I though maybe it would help step down the 170v, by giving the main ISO transformer 80v instead of 120v. Plugged the main ISO transformer into the black ISO transformer and presto !.. I got 110v - 115v AC.
Sounds like the mystery transformer (the extra one) is a step-down (or is overloaded), and the big one is wired in a step-up configuration. My MK2 transformer had an option for 90V in, IIRC.
Check the wiring for that big Williams transformer. Trace everything out by hand if you have to. A connection table for various input voltages should be in the manual for whatever game it was originally made for. If you set it appropriately for your local line voltage and no outputs are overloaded, everything should work just fine. When you moved that wiring around, you may have adjusted the set input voltage.
It is possible that some other strange issue is at fault here and is causing the outputs to run low, and somebody chucked that extra transformer in as a quick fix to "make it work now". It would be far better to resolve the actual issue if you can find it. I see that the big Williams transformer has lots of extra outputs. If any of these are overloaded, it can cause problems on other outputs. Check everything. Note that with no load, transformer outputs do tend to run a little high.
I hate to have excess transformers in a power path. People often install them without regard for spec. I actually yanked one from a machine I bought which was converted from 230V to 120V US use that was maybe spec'd to run at best the monitor. I'm surprised nothing had caught on fire.
If you do want to continue running it in the configuration you have with the multiple transformers, make absolutely sure that the extra transformer is rated for what you are using it for. Note that VA != W due to an annoying little thing known as power factor. If a transformer is overloaded, it can become rather hot and cause a fire. That would be bad. I've seen LOTS of transformers installed without regard for specs in arcade games, so don't make assumptions that it's OK.