I have programmed well over 100 2500's and 5000's, with the W head and the -O- head, all through the mic jack, never had a problem.
But I guess I could go ahead and dis-assemble the unit, and, solder my connections on inside, and program it that way as well
, but I prefer to eliminate any chances of getting the data corrupted, hence my saying to use the mic connector.
If the rear connector programming is working for you, then that is great, especially for the units in the console. But, the way I read the OP, is that he is planning on making his own cable, as opposed to purchasing anything, probably not the best solution with these radio's, as M equipment tends to get corrupted rather easily.
Factory programming cables are cheaper than a trip to Mexirola's Depot facility.