Because I put a 907ie rear swingarm on my 906 I also put the 907ie type brembo on, but I seem to have a problem with the brake seizing.

I think it might have to do with the cylinder because I blead the brakes for some travel in the foot brake leaver and after a small amount of driving that travel reduces until I think the pads are rubbing on the disk. After more riding the disk get hot and it siezes. I have to wait till it cools and crawl back home.

Is this the cylinder or something else? Any help appreciated.

Did it work with the old setup ?
I`d think about the caliper. I`ve seen a few in the past which pistons hardly moved. In many cases due to dirt entering caused by defect dust seals (often when the pads are about worn and the pistons have to travel out more). There`re rebuild kits, but I`d have that done. In many cases though it`s cheaper to get a new used one. Used rear calipers aren`t expensive.

other possibility
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G.

If the caliper is new, it`s unlikely, true.
My rear brake never locked, but when I opened the rear brake pump just to clean it I noticed it was full of some bluish crystalline stuff probably build up from old brake fluid over time. (When I rebuilt it I didn`t change the seals btw). I wonder if this could clog something up.

G.

I mean inside the pump. If I remember well there`s a circlip on the bottom side that needs to be removed to get the piston out. I`ll have to check where my spare pump is so I can make a photo.

this one was rather clean. One can see a little of that stuff on the last pic. My first brake cylinder was full of that. To push the piston out use air pressure or a thin wooden or plastic rod that goes through the small hole on the upper side of the brake cylinder. Anything else could damage the cylinder wall and cause leaking. To reassemble put some brake fluid on the seals and push the piston assy gently in while rotating it. Even if your brake cylinder is dirty inside I think your actual problem lays elsewhere.

your brakes locking up may be that you have a bit of moisture in your brake fluid, this happened to my ford F250 a few years ago.
PS: romus...you must be using the same hairdresser that I go to

There is a very small return hole in some master cylinders which will get clogged and cause the brakes to lock up. I had this happen on the Brembo system on my BMW. I cleaned it with a small wire and it worked perfectly from then on. Bleeding air into the system also worked until the brakes were used several times then they locked up again. So the cleaning of the return hole is the only real solution. It is easy to do but one must take the entire master cylinder apart .

The other possibility is that the piston in the pump is not returning far enough to uncover the return hole that dewjantim refers to. Sometimes , in an attempt to reduce the initial pedal travel riders have adjusted the brake rod so it is to long and it then when the brake is released it doesnt open that return port, and as the fluid heats up it expands thus opperating the brake , which gets hotter and the brake jams on even more .
I once followed a guy on a crapped out XS750 ( work mate ) the length of the west coast , who had made this "adjustment " and would not be told . I cant remember how many times we had to stop to pop the bleed nipple and release the pressure, and it nearly came to blows , but eventually the wheel locked 1/2 way round a corner and down he went, smashed the points cover and the timing plate behind it ...... so I left him there

...totally agree with McTool...

I adjusted the pedal height and managed to seal off the return bleed - result: locked rear wheel

I made a post on this one a few years ago; maybe the message needs to be reinforced!!
viewtopic.php?f=3&t=2342

VERY VERY dangerous - particularly if there's a truck up your ass!!

in fact...it did cost me a set of pads AND a rear brake hose; the hose had ruptured due to over-pressure!!
...took ages to find that fault; the rear was always a bit spongy but after 10 attempts to bleed it I finally saw the hose was bulging on the outer casing...there was some braking pressure but not enough to be considered a proper rear brake.

note: it might be possible to get the same problem by incorrect arrangement of the master cylinder components - the piston has the return/supply holes that need to be free to allow fluid in both directions when the brake is not depressed.