A 545 Allison has no overdrive gear:
http://www.messb.com.my/allison_at_545.html , so I hope you like going 55 MPH or less. You want to be at 1700-1950 RPM when cruising. After 2000 RPM, fuel consumption jumps greatly. Best fuel consumption to power is around 1700 RPM. You maybe could get away with big tires and a tall diff gear (what the stock busses that the 545 came out of had). It will be slower off the line and stink off road, but you could do 65-75 MPH (maybe, check with a gear calculator).
Stock, the BT series is done at 2600 RPM (defueling point / redline), so you cannot get away with a 1:1 ratio top gear like you can in a gasser. You have to get your gears (rear diff and transmission) and your turbo sorted, or you will get crappy fuel mileage and the vehicle will be a dog to drive. Use an online gear calculator to figure out your final drive line ratio for each potential driveline you evaluate. Figure out your RPM in each gear as well. I can send you my gear calculator done in LibreOffice Calc (Excel compatible), if need be.
I would look at different transmission options if you are married to the 4bt. I went with the ZF-5 manual, as I had a 4BT with a Ford small block pattern and wanted a manual (for better mileage and simplicity). You could also look at the NV series if you want a manual. For other automatics, you should look at the Dodge RF series that came behind the 6bt's. Realize, that you may need to replace the torque converter in it with one setup for a 4bt to get the best performance (you have two less cylinders than the 6bt). Further, the 4bt's came with many different bell housings, and if you don't get a 4bt with the right housing for your transmission, you will probably have to swap the housing for one that matches the transmission you go with (or buy a crazy expensive adapter from someplace like DeStroked). Factor these costs into your engine purchase decision (it is likely better to pay more for an engine with a bellhousing that matches your transmission, if all other things are equal). You might also want to find a shot in the butt Dodge Cummins RAM for parts... You can resell the 6bt in it to get your money back and use the rest for parts (including swaping the bellhousings and reusing the transmission).
Warning: Note that some 4bt's came behind TH400 automatics and have a GM adaptor bellhousing. Don't get suckered into using a GM car transmission. TH400's are just another non-overdrive transmission, and it is marginal behind a 4bt. The newer descendants of the TH400 have overdrive, but are still car-grade consumer transmissions and they do not live well behind diesels: avoid "car" grade automatics all together. Avoid the temptation of trying to hop them up too, your money is better spend on a real truck transmission than on trying to polish a turd. I mention this because every transmission shop in Amurika will try and tell you that a TH400 is Gawd's gift to the world, and they can built it to live behind a 1200 HP race car, so it is fine behind your little diesel. B.S., they may know alot about TH400's, but they don't know about diesels.
Your Dana 44 front is marginal for 35 inch tires, diesel torque and weight, and offroad use. Fine for on-road, light off-road use. I would put a 14 bolt or some other full float rear axle on it and ditch the 44 rear. They are cheap, and there is no reason to keep a 44 or AMC 20 rear with diesel torque: if you hop up the motor over stock, you will eventually break the rear (and you will hop it up... don't kid yourself) . While you are at it, you want to look at anti-torque tube's on the rear axle at least, if you don't have them already. Without them, the torque will s-bend your rear springs enough to pretzel your drivelines and kill your u-joints.
There is little wrong with your original Duramax plan, assuming you have the money to pull it off and the shop you hire is competent. It is lighter than a 6BT, and makes really good power. You have to spend lots of cash for it, it has electronics to putz with, and certain ones are better than others for longevity and swap ability. You could also put a 6bt in there, but the fit is tight and it is really too much weight to wheel/offroad with it (it is 1200 pounds with the motor over your front axle, and the bt series motors are very tall). Don't count out the 4bdt NPR Isuzu motor either.
Oh, check out the 4btswaps site. There are examples of 4bt, 6bt and NPR swaps into FSJ's and other similar vehicles.