Do you run with the hard top? If so, there is a way to mount an NMO on it, but it's a bit of work. You essentially make a ground plane on the inside of the top and secure it with some sort of adhesive. Then you drill the hole through the ground plane and fiberglass top. They make extra long NMO mounts for such applications. It can be done really professionally, but it does require planning and being very careful.
If this is for a VHF/UHF ham radio I'm wondering why you're SWR was so bad. I've installed a lot of smaller dual band antennas on Jeeps with hood mounts and never had a problem. Perhaps it was a problem with the particular antenna you used. I've used a small Comet B10NMO very successfully on Jeeps. Also, there are two types of "hood" mounts. One slips over the edge of the hood/trunk and tightens dows with Allen screws, the other mounts under the hood. I've used both, but the under hood mount is really easy and when used on the drivers side, about a foot forward of the hinge, it is fine as far as exposure. I had one on my Jeep and ran my radio at 5 watts most of the time. On a few occasions I cranked it up to 15 watts and that was all I ever needed.