(Side note: whats wrong with overkill?)
If you use a gear box that is bigger than what you need, you are wasting horsepower. The larger gears take more power to turn because they are heavier and have more friction. You also carry the weight penalty of the larger box that causes a decrease in performance as well. As with any build, the idea is to get as much power to the ground, in as light a package as you can.
A TH400 is overkill for a small block making the high 200 to low 300 horsepower numbers you said you where shooting for. The TH400 also doesn't have overdrive. Fuel mileage would suffer. I gather that you want to keep the stick trans you already have in hopes of saving the money on a new trans purchase. Nothing wrong with that.
Your choices on a divorced case is limited. The Ford 205 may be the only one with a left side drop. I think the IH case is right side and so is the Suzuki case used in the Samurai. Strength will become an issue with the Samurai case. I have seen them hold a 4.3/200-4R combo, but don't know how much more they will take. I think there is an after market kit to divorce a Toyota case? With all of these, your electric speedo would need adapted.
I still think a married 231 would be the best choice.
The only wheel base issues you will have is front drive shaft angle. Your wheel base should be about 123"(That's not "short"). You don't need or even want a short trans/case combo. Your extended cab gives you allot of room to get things moved back to help with front shaft angle issues. The use of a reverse cut front axle helps the front drive shaft angle because the pinion enters the axle higher.
An after market kit to divorce a Toyota case and Toyota front axle might be an option like M&M suggested..........I don't know what you'll get into with steering and such. Cost may be an issue as well. The D30 swap works well because it bolts up easy and the Jeep used a 231 like the S-10, and there are no major issues with steering hook up. Dan