OK, not sure where to start here. I took a close look at the radio, the headset, the cable and the antenna, and there are a number of issues that pop up, some safety issues and quite concerning…
The Audio issue:
The DB-25 pin connector on the back of the radio allows for such things like headsets and different audio level inputs. In the programming software there should be settings somewhere for adjusting the levels. Since I don't work with Vertex radios, I'm not going to be much help. I know where the settings are on Motorola and Kenwood radios, but that isn't going to do you any good. You need to talk to someone with Vertex programming experience. The guys at Rugged Radios should be able to assist you.
Purchasing the hand mic isn't going to tell you much as it uses a different connector on the side of the radio, not the DB25 on the rear. The settings for the audio inputs are not radio wide, they are for specific inputs. The hand mic isn't going to do anything to prove the proper function of the DB25 connector, the headset or the interface cable. All it's going to tell you is that the microphone input on the side of the radio is working.
Antenna:
The problem you describe is an audio issue, not an RF issue, so the type of antenna isn't the issue. Changing out the antenna from the Larsen you have is probably a really good idea. The Vertex VX6000 runs 100 watts on UHF. The Larsen antenna you linked to is only rated for 35 watts. Even if you have the power turned down to 50 watts on the Vertex, you are still looking for some issues. Antennas can overheat if hit with too much power, causing damage. The Laird antenna you linked to is rated for 100 watts.
100 Watts:
Wow, this is an issue on many levels.
First of all, running 100 watts on an ATV is exposing your body to unhealthy levels of RF energy. To be safe, you'd need 6 feet of separation between your body and the antenna to be out of the danger zone. Even turning the power down to 50 watts likely is unsafe. RF energy at that level causes tissue heating, and that can lead to all kinds of issues. Seriously, not trying to bust your chops, but this is dangerous.
The other issue is that while you are pumping out 100 watts out of the radio, your antenna is really not doing you any favors. These low profile antennas are really poor performers. Getting a more efficient antenna up and in the clear is going to help things a lot. The antenna needs to be unobstructed, by you, the ATV, etc. for it to perform well. Mounting it down low on the rack is going to make performance suffer. Also, a 100 watt radio is going to tax your electrical system if you do a lot of transmitting with it.
I'd really, strongly, suggest turning the RF power down as low as it will go. Get the antenna out and in the clear. High RF power isn't going to overcome antenna deficiencies, and it does nothing on the receive side. These sort of high power radios are intended to be installed in cars or trucks where there is sheet metal between the antenna and the occupants. Using this sort of set up on an ATV is not safe.
Even on my UTV, I'm running 25 watts to an antenna mounted on the roof, with a layer of metal between me and the antenna.