You can't add codes to Harmony like you did with Pronto. Best you can do is email the codes to support, and they will add for you.

X1 is XMP protocol which is nearly impossible to learn, but the pronto hex should work fine. I don't understand why it's not working for you.

I find JP1 remotes the most flexible in terms of codes. You can add any codes or protocols you want, even those of your own design. And they are very cheap.

Otherwise, URC or a tablet based remote like iRule is probably your best alternative.