I know I'm a little late on replying to this but figure people might look this up in searches. There is quite a bit of not-so-accurate information listed on this. Here are a few comments.
M1009 - based on a Blazer. 6.2, TH400 trans, NP208 t-case, 3.08 geared 10-bolts with a rear Gov-loc. (no 12-bolts or any other gear was available)
M1008 - based on a 1-ton pickup, only difference are the axles are 4.56 geared D60 in the front, and a 14FF rear with a Detroit. As far as I know there was never a M1008 with any type of "locker" or other traction aiding device in the front. There were some other variants like M1028 and others (pickup with speciality bodies on them) that had the Trac-lok limited slip (not very positive engagement).
I don't believe the 700r4/4L60 will directly swap with the TH400 in regards to the input shaft on the t-case. The TH400 version of the NP208 t-case uses a 32 spline input, the 700r4 version uses a 27 spline version. I do think the 700r4 is a nice trans to use behind the 6.2, and was the civilian offered trans in 1/2 ton trucks and Blazers. I have a '90 with over 100k on it with the 6.2/700r4 combo with no problems, and the last 10 years it has been used and abused off-road. However I wouldn't put a 700r4 in the M1009 and keep the stock 3.08 gears because OD would be completely useless (way too high of an overall gear).
A stock M1008 can go faster than 50 mph. On paper with 31" stock tires, 4.56 gears, 1:1 trans gear, and 3,600 rpm governed speed of the 6.2 you would top out at over 70 mph. I wouldn't want to drive it like that for long periods of time, but it probably wouldn't be too hard on the engine.
"J-code" versions of the 6.2 are NOT military specific. All civilian trucks with the higher GVW rating had J-code verions (no EGR valve) simply because they had a high enough GVWR to lighter emissions regulations. Civilian1/2 ton trucks and Blazers did come with the C-code version, which again just added the EGR valve in the intake manifold. I have modified my stock C-code 6.2 to a J-code version by removing the EGR and swapping intakes out. There is some debate about which versions or year had better heads but have never heard any solid documentation to what is better, just's lots of hearsay.
While the 6.2 is no power-house, you can get a pretty decent power boost by simply optimizing the timing on the pump and increasing the fuel rate some (just be careful not to overdo it). Freeing up the exhaust and intake allows for more fuel rate increases.