Communications issues between Ardupilot and Computer
This sounds more like a networking issue than an electronics issue and may be better asked at that kind of forum.

My instinct is that your wifi bridge is corrupting the trunked serial stream, this could be a number of things, for example packet size.

The way forward would be to use something like wireshark to see what's happening at a network level.

Good luck with your project, it sounds fun!