In this case, where they've made a mess of both connectors and wires, I'd just cut the wires loose, recrimp, and put into new housings. You can get parts from GPE.

https://www.greatplainselectronics.com/products.asp?cat=86

You have a mix of 18AWG and 22AWG wires. Since you'll be crimping two wires into one contact, I'd use the larger contacts for both 18AWG and 22AWG.
08-52-0113

It still would be a good idea to get some of the smaller ones in case you're not getting good crimps on the 22AWG wires.
08-52-0125

Housings are at the bottom of the page. Get the ones with the right number of pin locations. You should also get some of the key plugs and key the connectors appropriately.

Finally, you don't need the crimper listed there. You can get inexpensive crimpers lots of other places.