Can the 15 signal limit on these be removed? It makes it impossible to send all of the logistic network signals into a factory.

Circuit connectors are very bad for your UPS, every signal is expensive, and I can't make that better because it's an issue with Lua itself being slow in that particular situation. Trying to send all of your signals through a factory building will certainly result in lag spikes and slowdowns. Instead of that, consider using some arithmetic combinators, placed outside of the factory, to select only those signals you actually need inside the building.

I have used that to some extent, but I'm trying to make an inception system that has the whole base (short of resource collection/storage and defence obviously) within a single MK3 factory. Controlling it needs circuit signals for every item though, or it just keeps producing them forever.

Still, I think I've found a solution in the form of "Skandragon's Radio Telemetry". It lets you transmit wirelessly and doesn't seem bothered by the fact that the receiver is on a different surface.

Try using provider/requester chests in balance mode to transfer the things you don't need in large amounts.