MDS, VVT, and transmission options?
Short answer Yes and No. MDS is not enables on six speed Mopar Challengers from the factory, so NO MDS cannot be used with any classic transmission. If you want to run MDS you'll need to do the floor surgery and install a late model transmission along with the appropriate speed sensors.
As for VVT, if you run a factory computer VVT is an option. Contact Hot-Wire about the various options for running a late model VVT equipped engine.
The aftermarket is on the verge of standalone computer that will enable VVT. Megasquirt is capable but I don't think anyone has gotten it to work, YET.
Hope this Helps,
Regards,
Joe Dokes