they dont fit as you have identified, the coils get in the way firstly, however you can make them fit with abit of jiggery pokery, i used to run a 996 bip track bike and have modified the panels to fit my 996r for track days, still to awaiting the first track outing so cant comment on running temp.
to make them fit you need to either relocate the coils (one idea) or cut off the air scoops that foul on the coils, howver you will then probably find that there is a bit more mdification required around the belly area to trim aroun the larger exhaust bore and low lying testestretta engine shape, unless you have the panels modified to fit a belly pan, which i do not, it sounds like lots of fiddling and maybe it is better to just buy the correct pannels, however i found it fairly simple with the correct rotory cutting tool.
you may be able to use other tools to cut the pannels, if you need to borrow tools depending where you are Id be happy to help out.
ps I didnt have any probs with the pumps
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