That setup should be making somewhere around the low to mid 50's, stock the 660 puts out around 33-35 rwhp. Find out what a stock bike makes on that dyno, if that other bike was only making 41 hp then the dyno is certainly reading low or they don't know how to tune bikes.

The guy you spoke with is clueless if he thinks the LTEs need to be replaced with a yoshi. Ignore any doubts thrust upon you about the exhaust, you've got an excellent setup it just needs to be tuned.