After certification you can do whatever you want.
For original certification you must go strictly by the plans.
Paul,
For original certification you are held by FAR part 21.191(i)(2) which references 21.193(e).
You are only required to meet these limitations for certification. After that you may make any modification you desire as long as the mod does not take the aircraft out of Light-Sport operating parameters.
I know this doesn't make sense, but I have discussed it with the head honchos in Oklahoma City as recently as this month at our annual DAR recurrent seminar, and this is the current rule.