If you are looking for a universal remote, you can check out Hifi-remote.com, and go into their forums. The host has some One-for-All URC-6131 remotes that he has added the JP1 connector and some memory to. The nice thing is that he has a complete Dish mapping that works rather well that he can preload into the remote or you (just tell him up front that you need it).
The URC-6131 has a full set of PVR buttons, as well as arrow keys, guide, info, and just about all the other things you would need. And for the few things it does not have, you can easily move that functionality onto an unused button (for instance, I have Page up/down on the Channel up/down, since the channel up/down on the Dish remote is on the arrow keys).
It's around $25, and will control everything you own (and you don't even have to get into the JP1 modifications for most of anything you would need to control).