Rob,
I didn't discover the interference until after the fact.  To get around
the problem, I use one shorter screw in the location of the rocker cover
(#1 cylinder).  It ends up just about flush with the end of the nut
plate rather than protruding like all the rest.  I know this violates
the rule of X protruding threads and I certainly wouldn't do it on all
or even just two adjacent screws, however in 900 hours it has yet to
loosen.   I also dimpled the forward rocker cover to guarantee
clearance.
If you increase the spacing, you may develop bulging between screws
over time.  Even at 5 inches you'll see some of this.  Unlike with the
ailerons and flaps, the wall thickness in this area does not provide
much stiffness between the screws.  I am in the process of building a
new cowl with variable wall thickness to eliminate this and other
problems with the original.
Depending on your exact clearance you may get away with just the
shorter screw or just the dimple.
Good Luck!
Chris Zavatson
N91CZ
360std