Did you get it working?

3.8 and 3.9 are new builds of the betta OS. There is not alot of difference other than having the latest and greatest.

So between the three rom choices...

Base is just that. A very basic stripped down 6.5.
Vanilla is the "standard" 6.5 with alot of extra goodies packed into the rom. (basically its the base plus a ton of other great stuff)
m2d is a touchflo esque interface. It is essentially a replica of the HTC touchpro's touchflo interface but built in to the 6.5 OS.

Personally I am using vanilla because of all the apps and what not included. And then i took the m2d cab from the file repo (2nd post of his 6.5 thread) and installed that over vanilla. The benefit here is that the m2d rom is very stripped down. Its just the base, plus the afora mentioned cab. With my set up I get all the vanilla goodies, plus I get m2d. I have the freedom to switch at will between the m2d theme and the "default" titanium theme.