The last kicker I had, I ran separate fuel pickups from both of the engines, directly from the fuel tank, which elevated any possible problem from one engine drawing fuel out of the other. And, I have had that problem in the past.
I am assuming you do not have a shut off valve to sperate the two? That would be the easiest, as you could just turn off the valve.
If you have a portable tank? You can hook the "kicker" fuel line directly to the portable tank, and plug where it went into the filter. At least that would tell you if the kicker is sucking the fuel from the main? If you have one fuel pump strong enough, that can happen.
Have you determined if it is "flooding" or "lack of fuel" problem? I think it is the later, but if not... you have a completely different issue?