It loads fine for me in 64-bit Windows. It's a command-line application, so you can't just double-click it. Check out a tutorial on how to use command-line applications in Windows.
But you should really just avoid broken roms from the start. There is no need to fix cleanly dumped roms. I checked USA version of Ninja Spirit from the no-intro set using pcetoy and it's not encrypted and works fine on my PC Engine using the TED 2. The no-intro romset isn't perfect for PC Engine, but as it doesn't include any hacks, it's at least better than the old goodtools romset which includes all kinds of broken shit.
The PC Engine is sensitive to mods though, so the jail-bar mod might be causing problems after all.
You may also want to try elmer's OS for the TED 2. The original OS apparently breaks some games.