John,
Is your antenna from LMC an original-style antenna? There is another discussion of this topic in the Paint & Body Shop Forum - with a photo of the template/instructions and a photo of an installed antenna:
http://www.stovebolt.com/bboard/cgi-bin//ultimatebb.cgi?ubb=get_topic;f=4;t=002184
If you drill the hole as shown in the template, the bezel (and seal) will ride up a little on the "belt" on the cowl (at the cowl crease-line, labelled on the template).
You are correct to be concerned - drilling a hole is a "point of no return.
Good luck,
Tim