I cut most of my clearance holes by mounting the panel in the drill press with an appropriate sized holesaw and the panel angled similar to its position in the car...or, if the panel was part of the car, such as the dash or cowl, I carefully marked the postition of the prospective chassis tube and used a holesaw in a portable drill to make the hole, egg-shaping it if necessary with a die grinder and carbide bit...
If the panel has to slide around the rollbar tube, slotting it to fit and then making a cover panel to cover the slot would be in order...this can look quite sanitary and stock if carefully done...
I've made the end hole with a holesaw and the slot with a saber saw.
If you could share a picture of the end location and the panel position, I might be able to help further.
I've only done panel work on race cars so may not be familiar with the location you describe since roll bar and cage members usually attach to subframes and chassis members on race car chassis...
Pat
http://www.jps.net/binay/webdocs/strtmstng002_sml.JPG
