are you running a plug cap with a resistor in it? that could help. or maybe thats not where the interference is coming from?
what are you riding? if your ht coil is real close to your magneto (if thats what youre saying is causing it), perhaps you can relocate the ht coil so that the pickups are farther away. whatever is causing it, find out and move your ht coil far from it.
in theory you should be able to wire your ht coil up on your rear rack, under your fender, in your gas tank, where ever you want as long as its grounded and wired properly. itd just be kinda goofy having all that extra plug wire. but hey, if it works it works, and it seems like it could be worth a shot.
not sure how much resistance the extra length of wire would add, but i wouldnt expect it to be a lot and youre only talking 3-4 feet of plug wire tops. dont think itd have an affect on spark.