The rules don't really specify that developer intended skips are not allow so just in case since I had a bit of a scare before is it allowed to skip level 1 - 3 in run 3 or no? (Also does anyone have any recommendations on which versions to use for run 1 and 2 since I haven't run those games at all.)

sorry for the late reply, didn't see this until now. I guess you can skip them cuz you did on the run 3 main boards. For run 1 and 2, we use .swf files in the standalone player (i can upload them for you if you cant find/ download them online).

Standalone Player Link: http://www.flashflashrevolution.com/vbz/showthread.php?t=120256

If you have any questions about run 1 and 2 100% feel free to ask.