My only real concern is gearing, short of a second t-case, or Sammy axles. what options do i have?
It has 31's on it now...

It currently has 4.10 gears and a 10% lower transfer case.  Depending on the transfer case though, you will not be able to swap in the lower T-Case gears.  And your axles are going to be hard to find if you break one if it's not already running Samurai.

I'm running 33x12.5" tires with a 6.5:1 transfer case and 5.12 gears.  I can't quite hit the stock listed top speed, I max out around 52-55.  Stock it would supposedly do 62 or so. 

If you can find any LJ80 diffs will lower the gearing around 20%.

I think ive decided to swap the 31's onto my ammy for its 235's, and put the sammy t-case in sj410, with the mini lobster sj410 case in the sammy. Then run a 1.6 in the sj410. The Sj410 should be able to spin the 235's with twice the stock HP and a little higher gearing... plus the sammy is the off road truck and the sj would be the dd.

I believe you will need to do a transmission swap on the 410, I'm pretty sure the 4 speed has a different bolt up then the 5 speed from the 1.3.

The 410 transfer case brings a Samurai back into stock gearing for 235 tires. 

I believe you will need to do a transmission swap on the 410, I'm pretty sure the 4 speed has a different bolt up then the 5 speed from the 1.3.

Yes and you'll have to cut new shifter holes in the floorpan too.