Rear Brake weak

Hey all, I have a 79 KZ1000 shaft, with rear disc brake. I've taken the master cylinder apart, inspected it, replaced the brake fluid, and rebuilt the caliper (both pistons).

I've bled it thoroughly, but no matter what, i always have a weak rear brake. If i apply it as hard as i can it barely slows the bike down, hardly any brake power. It seems like there is air in the system to me...has anyone else run into this? am i missing something?

If the pedal travel is excessive, and soft, then I would suspect air in the line. Otherwise possible hose defect, or the caliper mounts slide pins, are they free and lubed? Then of course some replacement pads are junk, no stopping power. What are you using for pads? I use the Bronze double H sintered from EBC. They are a bit more than the cheapo pads but stop really well and are completely free of noise.
How are you doing the bleeding?

The slides are free and lubed...the pads have not been replaced...they are original (only 1000 miles on the bike lol) Should i consider fresh pads ( i was actually looking at EBC), the fronts are original too and work pretty well.

First, i gravity bled it. Then I pumped the pedal and while holding it down cracked the bleeder valve, closed the valve, let the pedal back up. repeated 1,000,000 times... with no difference.

What should i look for with the hose? Bulging?

Bulging, and excessive flexing.
so how far does the pedal travel, and does it get firm, even at the end of its stroke? When riding does it improve with several quick pumps? How about the push rod adjustment, it only needs like 1/8" of freeplay.
Only 1000mi, well my next thought was a rotor to thin/ under spec, guess that would be OK.
Is it possible that a seal from the rebuild kit is incorrect or miss installed? Wrong diameter?
when pumping and hold then open bleeder, do you get a good fluid delivery? Reservoir goes down after closing valve and pumping again?

It does not seem to improve with multiple pumps. I'd say 3-4 inches it goes down, i will go out and measure it and free play tomorrow. As well as observing the hose.

It never seems to get firm, it simply wont travel any further.

It is possible the seal is incorrect but unlikely, they are the same as the front-and the front work perfectly. Plus, it did this before i replaced those seals... The fluid flow is excellent, and the reservoir goes down.

Is it possible theres are trapped in the other cylinder behind the piston since there are two pistons and a single bleeder? I've even tried bleeding the bike at different angles to try to get all the air out.

You could take it off of the mount, place a piece of wood between the pads so the pistons stay out. Then hold it so the bleeder is the highest point, but hold the caliper lower than the master. then try bleeding again.