So I started the video conversion with the details provided in the above link (plan in my build thread in case you want all the info). In short, I purchased a USB capture card and setup an old laptop to process the flipping of the left video feed. Tested the capture ability and software flip on a DVD player via composite connection, and got everything working with no issues.
I then got my CGA - TV encoder:

Got everything hooked up correctly and first tested as a direct composite connection to my TV - blurry, and not flipped, but good (I plan to use S-Video anyway). But when I run the composite connection through the capture card:



Flipped, yay - picture, BOOO! I tried all the normal runs of testing (cabling, software tweaks) with nothing changing but the size of the mark on my forehead
So process of elimination leads me to believe the issue is with the capture card and/or SW setup on the laptop.
OR it's an issue with the video feed from the jamma board not being one the capture card can properly translate.
I did some more digging on the subject. Found some have had luck using a "jrok sync cleaner". Now my encoder is not from jrok, but it seems others have used these without having one of his encoders, also. My question is, how does this cleaner connect in line with the rest of this equipment? I've found no instructions on this device.

Is this worth pursuing in my setup, or should I go with a different capture card? I can get the same card that was used in the neo forums link, but that will require an actual desktop build, which I was avoiding. Would switching to an S-Video connection make any difference? (I wouldn't think so)
Any insight would be greatly appreciated.