If your TV responds to the same IR commands as the Zenith IQB50M90W (and I suspect that it does)there is a Pronto ccf file that I decoded and it looks like this TV responds to the same codes as the Hitachi HDTV's. If that is so, the recent Hitachi TV's do have discret input and power codes.
I don't know anything about the MX1000 but I did not see a utility to convert Proto files. Usually, that means that you get a One-For-All remote that can be programmed for discrete commands and have the MX1000 learn those codes. The good news if I am corrrect about all this is that you don't need a JP1 cable since the device is already in the OFA library.
If you already have an OFA remote then I can give you the complete set of Advanced Codes for TV_0145 setup codes. I do not know if your particular model will respond to any or all of the discret codes.
You might first check out the files or the MX1000 forum to see whether anyone has an existing file for your remote for the Hitachi HDTV with discrete codes included and try it.