Low SWR just tells you that there's little reflected power. It doesn't necessarily mean the antenna is working well, or radiating that RF well.
The metal under the antenna matters. That's the ground plane. Even though they may be "no ground plane" antennas, any metal under the antenna is going to impact performance.
Ideally, the antenna should be permanently mounted dead center of the truck roof. There should be, at minimum, 18" of metal in all directions under the antenna. Center of the roof, even on a regular cab truck will do that just fine.
Mounting the antenna off to one side will result in a lopsided ground plane and will make the antenna slightly directional (in both transmit -and- receive).
Mounting the antenna down on the fender will result in that lopsided ground plane. It can also result in some shielding from the cab.
Permanent mount NMO installed in a 3/4" diameter hole drilled in the dead center of the truck roof is the ideal installation. Cut coaxial cable to length and install the appropriate connector. Radio 12 volt DC power should come directly off the battery. Don't tap into existing wiring or cigarette lighter plugs. That's a good way to introduce noise into the radio via the power leads, and can impact performance.
The Tram antenna you mentioned earlier is a high gain antenna. That might look good on the surface, and may work well in some applications, but that extra gain comes with trade-offs. The gain is achieved by focusing more power at the horizon. That's great if you are out on the plains, and the truck is always perfectly level. Might be great in Saskatchewan, might not if you are in the middle of BC.
The Maxrad is a standard half wave, and while it has a bit of gain, it's not quite as extreme as the Tram.
Since you have two different types of mobile antennas, it might be worth getting a proper NMO mount installed in the center of the cab, and then comparing antennas. Likely you'll find one works better than others in certain situations. But that situation will change as the trucks move around. Your own experience will tell you what works better most of the time.
Sounds like you have a couple of things to address:
Duplexer tuning. -call a professional.
Appropriate coaxial cable. -easy to order the right stuff.
Increase repeater antenna height. Height is important, but I don't think you're going to see a huge amount of difference going from 30 feet to 70 feet.
Permanent install of mobile antennas. Always a good idea. No compromise mounts, no mag mounts, no fender mounts. Do it right the first time.