Thanks for the pics. If I understand correctly, the pink connector is the problem, because it's too wide (has two unused spots for terminals) and the mating key is offset. That is part of the factory wiring harness, and you don't want to modify it. I think what I would do is get this:
Buy CT21UV01 Car Radio ISO Harness Adaptor to bare ends (or the equivalent from another supplier). The one on the right of their photo looks to be the connector you need to match the Crutchfield harness. You can then de-pin both the new connector and the factory connector, and being careful to put them in correctly, snap the factory pins into the new connector. That would let you get everything hooked up without having to cut the factory harness.