I had the same problem with my '03 RKC. It had also sat for a couple years.
I rebuilt the MC, using the HD rebuild kit. That helped a small amount, but not tremendously.
I fixed it definitively. Here is what I learned:
If when you start the day, you have to pump it a few times to get the pads to the discs, but when you do get the pads there, they do not feel mushy or soft, rather, nice and hard at the contact point, you may have my problem.
If when you get to the contact point, and the brakes feel soft or mushy, you may have air in the system. Air tends to compress, fluid does not.
Now for my fix. I find that HD pads are chirpy and dusty. The dust gets in to the brake mechanism, and if allowed to sit, it could accumulate and bake a little bit, making a sort of crust on the pistons. The brakes do not have return springs. They depend on just a bit of eccentricity in the discs to push the pads off when not engaged. Normally, they will not push off very far, and will even kind of contact during normall operation, giving that chip-chip-chip sound that goes away when lightly applying the brakes.
Now, if for some reason, the pads get moved back too far from the discs, it takes more fluid to move them back up against the discs, like what happens when you pump. Once up against the discs, braking is positive and strong. How this happens is, if you have crust on the pistons, and the rubber seals around the pistons may hang up on this crust. The seals will stretch a bit, and allow the pads to move up to the contact point, but over a short time time the seals will drag the pads back in, and too far, and push fluid back up into the MC that normally would stay in the lines and calipers (staying in the lines and calipers and is how they auto-adjust for wear).
OK. With all of that being said, do as Bodeen said, and carefully extend the pads out so you can access the pistons. clean off those pistons with shoe laces and brake cleaner, till they are clean and polished again. Reinstall your calipers and test. You just may be good to go once again.
Just an idea, and it fixed me all up. Maybe you too.
Good luck,
Rich P