Yikes! You want to do all that stuff before you glue the wing skins on, e.g. the retract gear mounts, wheel well, air line channel, servo mounts and servo wire channels.
http://www.rcuniverse.com/forum/m_39...11/key_/tm.htm

Cutting the holes in the foam for the air lines and servo leads with a sharpened tube would be best at this point.