I would start at the back, Yes. Assuming that the kit is available to buy that way.
Others will have their own opinions on this im sure.
I remember years back being really impressed with an RST that had an Ahmed rear set up, which was in essence very similar to the MEF setup but with different shocks.
That extra adjustability at the rear which allowed for geometry to be set outwith the limitations of the original setup completely transformed the ride.
More recently I've been well impressed with Oli's (Red S1) which has the full MEF set up, front and rear, it handles like an rst ought not to.

Tony Im sure you'll read this whats your thoughts?? is Martin still doing the Kits? and is buying the rear seperate from the front an option?