Kevin,
Well, just looking at the output on the controller based web page gives one of the few views into the noise environment, but when I watch mine, I'm very surprised that the servers actually can extract some usefull signals out of the mess I see.
So you might just turn it loose and let it connect to the servers and watch a bit.
I think that the designers took complete control over their system, and if one station is sending pure garbage constantly, they turn it down or "off" by forcing an interference mode. The others here (the old timers) can comment more authoritatively, but I don't think that, even during initial setup, that there is a disadvantage to trying to send data. I don't believe the servers are bogged down or hurt in any way, which was one of my initial fears that I'd futz something up by trying to test and wanted to remain off line while doing so.
Second, my little external GPS antenna is sitting in doors , by a window, and sees a lot of satellites. For you to have to put yours outdoors and have difficult reception to me means you either have a LOT of surrounding stuff blocking the view, or a wee bit of connection problem. I assume you've moved it about and also taken the SMA connector off and reattached. But if you're getting a good report on the controller web page that enough satellites are in the green and being tracked, worry about that later.
Unless the other fellows say to NOT let your station connect to the servers, I think you'd be better off letting data flow. The servers protect themselves from sort of a (internet term) of Denial of Service attacks so to speak, and there are a couple very clever fellows here who peak at things to give very helpful advice as to what you might do during setup mode.
My LCD display worked OK, but I'd suspect that you didn't get the jumper right to correspond to the color of the display your have, or an errant pin was not making good contact when you seated it (or even make sure, and I'm not being critical here) that the display is indeed oriented correctly and not bass ackwards on the socket. To be frank, I've not looked at mine in a couple weeks, so I do all stuff except to do a reboot, via the controller generated web page. But for awhile it was nice to have, especially during boot up and all.
Oh, CONGRATULATIONS on the project! Now, the fun begins.