Hi, hopefully it wasn't too late to solve your problem.
I have bascally the same set up with you. I use helix effect instead of the helix floor because I'm using only the post effects and the main sound is from my Mark V 90 head.
The ground loop problem I have also encountered but I did not have the channle switching problem so I think you may have got a wrong cable or something.
You will need a
Stereo 1/4'' Male to two Mono 1/4'' Male Insert Y-Cable
something look like this https://www.rubbermonkey.co.nz/Hosa-STP-203-1`4-Insert-Cable-3m?gclid=CjwKCAjwtIaVBhBkEiwAsr7-c-Qlj8pkGdjp6WEwXi7JIZoVoKvy5-UEoW45VFT96OS5wYX_LgmdzxoC9ewQAvD_BwE
You connect the trs end (two black rings end) on the helix ext amp, and connect ring end and tip end to the channel 1 and channel 2 switching socket on the mark v.
You will definitly have a ground loop problem since you have connected the sleeve (ground）of the cable to the mark v. A simple solution is to disconnect the sleeve wire of the trs cable. you can cut it if your cable can be done like that. For my case, I'm using the cable I show you in the link. I cut the ring and tip end and re-solder in to a trs jack. Just make sure there is no connection between the sleeve wire to either the tip and ring end. In my case the problem is solved.
In helix, you can use ext amp switching to switch channels. Make sure it is set to latch mode. And the mark v channel setting is set to channel 1 (default channel).