Since you will be mounting on your rack, I would mount a Larsen 1/2 wave whip. The 1/2 wave antenna will give better performance since there won't be much ground plane for a 5/8 wave antenna (which would otherwise be my recommendation). Half wave antennas can still give decent performance in terms of SWR even without a ground plane (the coax acts as the counterpoise). In your set up, a 1/4 wave antenna will give poor performance.
I would also mount the whip of your antenna on a spring. Up high like that is great for radio performance, but it will bang into lots of branches and overheads.
If you do want to drill a 3/4 inch hole (not 3/8 as stated), an NMO mount centered in the roof will give optimum electrical performance and allow you to run a true 5/8 wave antenna.
Lots of other options-you could do a lip mount on the edge of the hood. That's not a bad compromise.
I've changed antenna systems on 2 trucks 3 times since becoming a Ham 2 years ago. In general, I have come to appreciate the simple, cheap, robust, and otherwise excellent antennas from Larsen. Plain steel whips seem to hold up better than other antenns in the offroad environment. If you want pics, I can supply a few later today.
Have fun.
edit:

Originally Posted by
Desertdude
Larsen NMO 2/70B - and a NMO 150B antenna when I can have something taller on. I have seen AndrewP sometimes uses a rubber duck on really tight overhead trails and close formation trips.
I like the antennas that DD mentions as well, and have a couple of the Larsen 150 series which are cheap and work great. They are cheap enough to carry a spare. I have run a shorty 1/4 wave Comet(SBB1)--Very poor performance, but good enough at short range, just not so good for working repeaters at a distance. It does work fine for trail use, and still blows CB out of the water. It's very flexible and does not hang up on trees.
Last edited by AndrewP; 12-30-2007 at 02:10 PM.
KI6MIE
Sacramento CA
1997 FZJ80 Desert traveller
1989 FJ62-OME, 33s, OME suspension, H55f
1984 FJ60-SOA, H41, toybox, locked, 37s, Rubicon edition
1971 FJ40-SOA, FJ60 axles, 85 2F, it abides