Actually someone has used JE building their Thruxton. Thrux-ton-up over at the rat.neet forums has recently rebuilt his ride using JE piston's and bill's 42mm carbs and lot's of other goodies. His bike is also on the mainpage of the 2001 bonnie forums at delphi.
He used the stock 865 bore size and had piston's made for the barrels. 11 to 1 pistons....apparently the bike runs very well :-)
