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First gear should be between neutral and second.   Are you having to hit the shifter twice to go from second to neutral?   Don’t mean to stay for obvious, but trying to ascertain if there is a click from neutral to first and then I second click to second  or if it goes straight to second….   Or is there a position for first but it doesn’t pull in first?

I dropped two ECU’s and a voltage regulator in the mail earlier today. Hopefully you will have them by the end of the week to use testing 

I didn't try to start it before I tore it down.  Guy I bought it from said it didn't pull, and already had the oil tank etc removed.    I did reuse the cam and tensioner.   Engine ran great after top end, rebuilt crank, new timing and oil pump chains.   That said, I either have oil pump or Hondamatic issues, because once I got good and hot (miles from home) the Hondamatic started racheting noises and didn't want to pull.  When the machine cooled down I rode it home without issues.  Luckily I had an extra engine on hand, which is my current "when I have time" project.    Keep in mind that like a 2007 Rubicon rear fender might be $300, a 2014 Rubicon rear fender is $157.   Different years had different part numbers, with the difference usually only being the sticker on the fender.   For example, a left side cover for a 2007 Foreman was over $100.  A left side cover for a 2008 Foreman was $29.   That's what you gotta look into.  Different parts will fit your machine, and nosing around is the only way to see if a different cheaper part will fit. 2014 and 2008 Rubicon fenders etc will be the cheapest for fenders for whatever reason.   But yeah, let's get it running first.    

I repaired the reverse control handle lever and it goes into reverse just fine. Lifting the shifter will let it easily go into second gear but pushing the shifter back down goes into neutral but will not go into first. It acts like it has no 1st gear. Does anyone know what is happening and how to resolve this?

So I've read through your post two times from last year, and eyed the pictures a bunch.  Did you reuse the camshaft and tensioner on that machine?  Also, did you find that the timing was off when the oil pump chain jumped off?