If your bandwidth is a only few 100 MHz, then some wiring oddities over a few cm will do no harm. As a rule of thumb, a transmission line discontinuity of 1/20 lambda long is tolerable. From my dim recall of communications theory, 100 Mbits/sec requires a bandwidth of at least 150 MHz. Lamda for 150 MHz is 2m. So a dodgy bit of transmission line no more than 0.1m should be tolerable. Well, yikes! I would never put up with such a mess at VHF. I am sure you can do better.

I should point out here that microwaves101 is dedicated to microwave topics, where interesting things happen at frequencies of many GHz, and physical features of fractions of a millimeter. On my own admission, I do not really belong here, as my RF expertise is in UHF (300 to 1000 MHz), not microwaves. Having said that, microwaves101 has provided many useful guidelines for my designs.

On a more practical note, the answer to the question "will it work?" is to test it. To me, testing means hiring some kit or a lab session to find out whether your non-standard connector affects attenuation, bit error rate, and so on.