Bronxxx, interesting project of putting that drivetrain combo into a FJ62.
The 6.5 turbo I've got is a built engine and really moves my 5500lbs Fj40 (this is with 3.7 gears)
If you can, get the Transgo HD2 shift kit for the 4L80e. Makes a huge difference on how the transmission works.
As for the 203, I'm taking it out of the truck this winter. I've personally had all sort of leaking problems with it. Also, because of the space constraint of the 40, I had to go to a 2 piece front driveshaft that I've never been able to get it to balance properly. So with no 203, the leak will be gone and I should be able to go back to a one piece driveshaft on the front. I know that Boots and Chicago here on IH8MUD have a similar drivetrains and have not had issues that I know of. For the off-roading I do, I've never needed the extra gearing. The low end of the 6.5 combined with the slippage of the torque converter of the 4l80e has gotten me as far as my nerves will take me and then some. I am planning on going back to 4.1 gears this winter as I feel that the engine is lugging around to much. Going back to 4.10 will bring my rpm's back up and I hope it will give the 40 a little more pep. The 4.10 will also help out in the off-road department.
For the 203, it all depends on what kind of driving you. I know the adapter for the 203 to splitcase is made by Advance Adapters but isn't sold by them. I got mine from Mudrack here on MUD. However, if you still plan on going with the 203 and are not it a hurry, my adapter will be for sale sometime early next year (probably February).