I've dealt with a similar problem on a cage brake system by removing the newly replaced M/C, bench bleeding it, and then re-installing and re-bleeding the entire braking system. I can't write intelligently about it, but some air was entrapped within the hydraulic system of the M/C itself, and conventional bleeding could not provide enough pressure (vacuum) to pull the air into a brake line, through the proportional valve, through a caliper, and out the bleeder. As soon as I plumbed the temporary lines back to the reservoir, and started pushing on the M/C piston, TONS of air was pushed out. Once re-installed, it was about 10 minutes of conventional bleeding and the job was done.
Now, I have no idea if that would (or could) work on the motorcycle. But the principles seem the same and I can't see how it can hurt to try.
This video does an excellent job of explaining exactly what I did - down to the minute detail:
I believe you mentioned that you have a mitey vac vacuum pump - if so, the hoses/fittings that come with that kit should give you what you need to do a bench bleed. If not, the hardware store should have it.
A word of caution!!!! Brake fluid (DOT 4 and below) EATS anything that is painted. If you decide to try this method, then you will be reinstalling your M/C full of fluid. When you remove whatever you have chosen to use as a plug from the line bore to install the brake line, some fluid is going to leak out. Keeping the M/C cap screwed on should reduce the amount of fluid that leaks out because there should be a slight vacuum on top of the fluid within the M/C. None the less, some fluid will leak out. In the light - VERY IMPORTANT - VERY VERY VERY IMPORTANT!!!!!!! - you will want to protect and cover anything that is painted and that brake fluid could come into contact with. Things such as your tank, fender, etc. Have a wet micro-towel handy on your seat. If you happen to get a drop of brake fluid on your painted surface, you can quickly wipe it up before it has a chance to eat your paint. Don't forget to wax everything after the job is done. PLEASE (PLEASE!!!!) heed this - I've seen some pretty nasty disasters from spilt brake fluid.