I'd personally just re-make the covers in sheet metal, rather than filling the holes. That way, if you ever wanted to use them for cooling ducts, or to put lights in, you could simply modify the covers to accommodate while retaining good aero, rather than giving up any potential future use of the holes by glassing them in.
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Call me crazy, but I actually try for mpg with this Jeep:
Typical driving: Back in Rochester for school, driving is 60 - 70% city
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