I'm not sure why you'd want the manual transmission, most offroad crawlers prefer the auto. The manual works, but you definitely need more low gearing to make them work. Also, I don't think the manual was available at all in the Durango or with the 5.9L in the Dakota.
Speaking of engines, if you have a choice, the 5.9L is the engine you should look for. It's powerful, reliable, easy to work on, and the parts are common and affordable. The 3.9L is reliable and torquey, but it lacks power on the highway. The 4.7L should be avoided, they run great, right until they don't. They suffer from very common head and valve-train issues. The 5.2 is a great engine, but the 5.9 is the same with more power. I think 1999 was the last year of the 5.2, the 4.7 replaced it. I don't know anything about the later 3.7L V6, but I believe it's similar to the 4.7 and would avoid it for many reasons.
The Dakotas that you are looking at were made 1997-2004 (Quad Cabs were made 2000-2004), and the Durangos were made 1998-2003. There was a mid-generation update in 2001. In 2001 they upgraded the interior, switched the transfercase from manual shift to electronic shift, changed the steering from a recirculating ball steering box to rack and pinion, and updated most of the electronics.
Durangos are very cheap and plentiful, their wheelbase is better suited for tight trail maneuverability. The Quad Cab Dakotas are about double the price of the two door Dakotas, but the extra interior space is great.
Since you are planing a solid axle swap you should examine the front suspension/steering differences between 1997-2000 vs 2001-2004. Don't discount the option of converting a 2wd. They are cheaper to buy initially, but obviously require the transmission to be updated to the 4wd output. I think the 2wd front suspension may be more difficult to SAS because of the frame shape. The rear suspension is also different. All Durangos (2wd and 4wd) use a common spring-under configuration. The 2wd Dakotas are also spring under with a shackle flip. The 4wd Dakotas are spring-over with the spring mounted higher on the frame. The spring-under suspension design is easier to lift with less spring arch. You could start with a 4wd and replace rear spring and shackle mounts from a 2wd truck if you'd rather convert a 4wd. My Dakota (factory 2wd) cleared 37" tires with a spring-over conversion, 2.5" blocks, and some fender trimming. I have eliminated the lift block by installing stock 2wd F150 springs because they are arched about 2-3" deeper than the stock Dakota rear springs.
Half ton axles are little undersized for 36-38" tires if you ever plan push it hard. If you do use a Dana 44/9.25" axle set with those tires like you're thinking, they will be your weak link.
For SAS swaps I can definitely recommend the Ford Sterling 10.25"/10.5" rear axle. It is a very beefy axle with decent aftermarket support. The Dakota uses a speed sensor in the rear axle to determine vehicle speed, many Ford Sterlings also use a similar sensor (my 10.25" is from a 1988 F350). The stock Dodge Dakota speed sensor can be installed in the Sterling axle after cutting of one small rib from the axle housing - it's a bolt in deal. With no speedometer correction my speedometer only reads 15% slow with 37" tires.
