+1 on most of this. 2-1/2 yrs ago when I installed my aftermarket unit I didn't yet know a source for a connector to match the harness. So on recommendation of my dealer, I did as Comancheflight did. Very easy because all wires in both the tractor and Pyle unit were well marked. Now that we can match the connector, I'd probably still do the same thing.
As for the factory speakers, I'm fine with mine. I'm no audiophile, but this is a noisy tractor, after all, even with the cab.

I also like to wear small, DIY custom-molded ear plugs (from Radians) whenever I'm working in the tractor, and just turn the radio up just enough so I can hear it. I've gotten much more protective of my hearing as I've gotten older.