If you go this route just toss a 1/4 wave on it. 6" vs 3" wont be noticed. I had run one of those on my Motorhome before I switched out to the LAIRD fiberglass stick. Worked fine for my application as I had no ground plane on the motorhome.
Just my opinion, while it will work, it is way too much hardware and effort to make the antenna system work. If you are going to insist on using it, use a Tram 1126B antenna to keep the height down
However, I would ditch the ground plane kit and just buy a half wave antenna, which is about 12 inches tall, or a 5/8 wave antenna and mount it on the hood or swing gate. The Midland MXTA26, which has 6dB of gain (32" high), is one of the 2 antennas I use. The other is the Tram 1126B antenna. Which one I use depends on where I am and what I am doing. They both work very well.
Also, why do you want to install this over the roof line? An antenna on the hood or swing gate will net you about 4.5 miles of range on level ground, while moving it to top of the Jeep will only extend range another 0.5 miles... maybe. Again, just my opinion, the cost and level of effort (not to mention appearance) its not worth doing an 'above the roof line' install.