I would likely do the same thing, but I would turn off all games except Juno First. That way it would boot right up to that game and seem dedicated. Having said that though, I can't really speak to the quality of the emulation on that particular game as I've only played it a few times on the 60 in 1.
Nice pickup!
I haven't seen a dedicated pcb in all my years collecting. Wouldn't know the difference on the 60 in 1 or not, but with the trend, I'm sure the sounds are different.
the PCBs do come up for sale (though they have been climbing in price) and Rich @ This Old Game has all the artwork available. there were some NOS joysticks (i think at arcadefixit.com) but they seem to be all gone now. otherwise everything else is pretty much standard stuff and a Konami to JAMMA adapter will run the PCB just fine.
the version on the 60-in-1 plays very well but like all the Konami games on that board the sound is a bit off. not bad if you've never played the original but if you have it will sound a bit tinny and dull. it's one of those games where the original sounds are really damned awesome.
good luck with a restore! i have two converted JF cabs and i need to buckle down and fully deconvert one of them.