I'd strongly recommend doing the secondaries when you are going to tripple filters (if you're going to do that). Getting the intake plenum back on the three throttle bodies as well as the two points behind at the same time was one hell of a frustrating job. Installing the filters at that time would have made it very quick and simple. Can still be done (I did it) but it was a pain.
By the way, removing secondaries really is easy. IF you drop a screw you're in deep **** ..... but it would be almost impossible to do that as long as you're careful. Make sure the primary butterflies are closed, tape up or put a small rag in each throttle body and use a magnetic screw driver. There were very clear instructions and a video on here but I can't get the link to work - maybe you can
http://www.r3owners.net/custom-mods/7958-how-remove-secondaries.html?highlight=butterflies
This thread also explains how
http://www.r3owners.net/rocket-perf...plates-butterflies.html?highlight=butterflies