I have a 4door 16V, I'd like to keep the tracker motor, but change up the drivetrain to get crazy crawler gears.  going for 31s  early january, but I'm goin to try for a d44 front and rear in the summer and some even larger tires.  Maybe even 40s

I hear good thinkgd about a sm465?  something like a 6.5:1 first gear    what setup would work the best?

What you want for 31's won't be same as what you want for 40's, They are going to be two completely different rigs.

40"? Seems excessive (and top heavy) for a zook. My 4-door on 35" went through the Rubicon with NO problems - would have made it just fine with 33" & armor. 40" won't survive long with D44. Toyota axles with Longfields are as strong as a D60. You're going to want dual t-cases for sure.

I figure the ratiowith 5.13 to 31s is the same as 5.89 to 37s If I'm to tackle a straight axle swap, I might as well go big.  with a high range reduction 40s would be right on

I'm not set on d44s, toy works just as well, depending which one comes my way first. 

yes 40s are excessive.  drove my 2door for 3 years on 33s, worked fine.then why?

why not?  never had anything bigger then 33s

5.125's aren't that great with 31's as it is, ideally they should be running the 5.83's imho. Keep in mind that even if gearing calculators show a comparable result you are turning much heavier rubber and that will take more power or more gearing for a similar outcome.

I'm not set on d44s, toy works just as well, depending which one comes my way first. 

D44 = Stronger than stock yota stock
Toy = Stronget with built (longfields) axles (as strong as D60)

Toy has lower ground clearance, but axle tubes aren't as strong (work around: truss the Yotas). Yotas have better disc breaks, and don't require an adaptor to thread up (same thread pattern as Zook). Aisin hubs are stronger than the D44.

Good D44 vs Yota thread here: http://www.zukikrawlers.com/showthread.php?t=13564