Nice rig. I wouldn't even attempt to modify it. As extreme as I would go is piping external audio gear into the data port thru an isolation transformer. Unless you spend a ton on rack gear the improvement is marginal. The mixing board with the crummy 3 band eq would be a downgrade IMO.
You can open up the bandwidth on a lot of yaesu rigs without modifications. Once done it will add the TTBF option to your bandwidth setting in the menu.
http://www.dk3hv.com/Equipment/FTDX-5000/ftdx-5000.html
Since you were looking at the heil website I thought I would mention my experience when I tried a pr40 and my ftdx1200. Works fine on ssb as long as the processor is on but the rig doesn't have enough preamp to reach 100% modulation on AM. Probably apples and oranges but just FYI.