1, No you cant run 2 CPUs at different speeds. (they'd both have to run at the speed of whichever is the lower clocked one)
2, The main board would be upgradable if only you could find the apple one (and if they change the board in the future it may come with a case redesign and thus leave you with certain location problems for the other hardware inside).
3, The heat sink used in a Mac Pro is different in size, shape and performance to the bog standard intel supplied one. This is why the Mac Pro runs cooler than an out-of-the box built clone system running 2 x Xeons with stock intel coolers.
3a, Most PC home builders would use a third party cooler (Personally Id never dream of using the crappy ones intel ship with their kit). In a standard PC case this isnt usually a problem, however in a Mac Pro the case is tightly constrained to an apple reference design so the choice of adding an aftermarket CPU cooler is going to be resticted at best, impossible at worst.
Tae the advice here and get the 2 CPU mdel now. Its cheaper, comes wth the apple warranty and even when newer faster ones come out - are you going to have to have them???
(This comesfrom 15 years PC experience of chasing the latest and fastest hardware as soon as its released - its tedious, expensive and to be honest unless you are Ray Tracing or High-end video editing; not necessary. The cool factor just isnt worth the hair loss - Thats why Ive just switched back to the Mac Pro myself.
Hope this helps .