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Sound like you got a bit of work ahead of you. The engine sucks to get in and out because of the weight. It will be easier out with the head off if you plan to take it off anyhow. If the bike is stripped, lay it on its side and pick the frame up. Easier to get a hold off rather trying to drag it out sideways. Put it back in the same way.

Try a sealmate tool to clean the fork seals. No leaks yet on mine 1+ year later.

Update 09/07/2017

When I first got the bike I spent some time on the rear master Cylinder, as it was in a troubling state. When I first disassembled the rear master cylinder the bore had a nice rust coating along with the piston, which looking back now, seems to be some kind of after market one. The seals were supple but questionable. So I Just disassembled it all washed it out with water and stored it in plastic bags to worry about later, I also had quite the time removing the rear brake switch, which didn't end well. You would think it is as easy as just pushing those two tabs in and pulling or twisting ... So I had resided myself to some sort of hydraulic rear brake switch at the time..

Jump forward to now, I have just had the chance to go through the spare parts that came as extra's with the bikes, and guess what I found another complete master cylinder. Still in a sorry state. So I tore into that hoping; for a good diaphragm ... well it wasn't; its in a worse state then the original one. The Bore on the other hand was in much better state. So I took the time to make a DIY honing tool; a close to 5/8 diameter piece of wood wrapped in 1500 grit sand paper with some oil. This was dodgy at best but did the trick. I tried the same on the other Master cylinder but had to go to 800 grit sandpaper to cut the rust off, its smooth now but still has rust in the bore.

So being optimistic I took the better of the two and used the original piston after some polishing to seem if it wouldn't leak. I rigged it up to a GPZ900r Caliper with some brake line from a Gt550, and it held pressure, regrettably I found out why this cylinder was spare parts the piston was worn or at least the seals.

This is a bit off topic, but I also had to do some brake work on my Z500 which conveniently uses the same 5/8 front master cylinder as the earlier Kz1300's. I had a problem with it not holding pressure and ended up buying an after market piston with dust cover. Which I soon condemned as bad and then proceeded to get a OEM one which was available from Kawasaki. When ordering the person putting in the order put in the wrong part number of by an increment of one, and when I checked it it was the number for the KZ1300 rear cylinder, see where this is going. So in the end the brakes on the Z500 were working, it was all related to the brake lever. Now I still had this spare aftermarket piston laying about for a year+. So when I saw the piston from the rear master cylinder I though too myself shit this is similar, and wouldn't you know it. The only difference was the end of the piston where the actuation rod slips into.

So taking a risk I took the seals of the aftermarket piston and slipped them onto the aftermarket looking rear MC piston. Slipped that sucker in the bore bleed the system and I had a non leaking working MC, I was so happy I decided to tear it all back down and sandblast the sucker and slap some black paint on. now I can write the rear master cylinder mostly off. Just need a diaphragm form it, thinking of getting some from that German site.

Below are some photos of the rear master cylinder after painting, not perfect nor is the Bore, still considering getting it re-sleeved possibly. For now it seals, and I have plenty of time to mull over it before the bike is ready for the road.

Very lucky, congratulations!
I just disassembled and cleaned both master cylinders. Unfortunately, mine have pitting and I am afraid I can't rescue them...
Big big problem.
I read that you considered re-sleeving them. I see you are in Australia. I am in Canada and I see our dollars are equal in exchange rate. I just called about doing just that, and I was told it cost about $440 per master cylinder. Plus tax would be almost $500. That's almost a 1000 for both master cylinders, and I think that would be justified if someone worked on an ultra rare hundred grand car. So far I found just this one place, and far from I live so I'd have to ship them as well.
Have you checked how much does it cost in Oz?
Does anyone who reads this have leads or alternative solution? A third party or using another model's master cylinders?

There's only two ways to fix these master cylinders. The logical way is to machine out and sleeve with stainless sleeves. Once they're done, they will never have to be done again and all of the original parts i.e. the piston and seals will fit.
The other option which requires a little more investigating is to machine out the bore and fit the next size up piston and seals.If it's a 5/8" bore, that's .625". The next easiest machining bore would be 16 mm which is .630". That would clean up pitting of .0015" deep, maybe not enough. One could go to 11/16" which would clean up pitting .032" deep or less. Then one has to find an appropriate piston and seal . Not impossible.
My preference is the sleeve.
Edit note- 5 minutes of research done to come up with this. Material to use for sleeving is 3/4" 304L seamless stainless steel tubing with a .065" wall thickness. Ream the bore of the master out to .748", Heat the.master in an oven to 400 deg. F. Drop in an appropriate length of the 304L tubing and let cool. Ream the I.D. out from the .620" tubing bore to .625" . done. That tubing is as common as Hen's teeth. The reamer is a standard over the counter size at .748" for exactly this type of work, preparing a bore for a .750" sleeve.

That sounds good and thanks for the numbers.
I don't have any access to machines, except hand drill and a grinder. No set up work bench, no vise. This time I am totally improvising and everything is being done by hand.
Some 30 years ago I had a set of adjustable reamers. I got out of engineering and mechanics pretty much 25 years ago, sold lots of my Snap-on tools and so on. I got my own bike again after many years, and got into taking care of it because often what I can do is cheaper and better than random service people. Especially the big brand dealerships. My local connections are very minimal, practically almost non existent, so I am pretty much a one man army, haha Anyway, I started feeling the old spirit and enjoying getting my hands dirty, and then this KZ came along.

OK. End of the side note. Just wanted explain a bit more me being nervous doing certain things in a not properly equipped space.

Good information! I will look into prices of reamers, although I am a bit nervous doing it by hand. Perhaps I will just settle eventually for resleeving both and having brand new like master cylinders. Well, if I would die and someone decides to keep it in the rain for 20 years, like the previous owner did, then at least the next person after that will not have to rebuild them!