On a side note I've been following this thread. Here are plausible solutions to the problems:
1) rusting in general: -Painting the rails after installation with rust resistant paint -Undercoat the body around the rails and the rails themselves after installation -Do both
2) Caps or no Caps -If capped, small holes should be drilled at mentioned above because they most likely will not be "air" tight. -If uber worried about rusing with caps drill holes and install small upward facing pipe to avoid water intoduction while allowing the hole for moistrue evapuration. -If uncapped, probably should drill holes alot bottom for drainage as water/dirt/road salt will get into the rails - Also regular maintance and ensuring dirt/road salt is not sitting inside the rails will prevent the worse corrsion.
thats my 0.02.
1998 SE Duratec V6 ATX
Ebay intake with K&N Filter
Trubendz Exhaust
Custom Hood