Warped brake disc

My 2 cents-  
Caliper pistons should float freely in the calipers when no seals are present. 
After installing the seals and dust boot, lubricate the seal and boot with brake fluid only NEVER any type of grease.
Install the piston and you should be able to press the piston to the bottom with a couple of fingers. if it takes more pressure than that, there may be a build up of crud, rust etc in the seal groove or the dust boot groove and will require additional cleaning.
Brake pads should float freely on the pins and in the guide areas of the caliper. If not, there may be too much paint on the sides of the pads.
Brake caliper piston seals and dust boots will swell if the wrong brake fluid is used. It's very important to never expose the elastomers to the wrong fluid. I've seen many brake systems contaminated by owners topping up their brake fluid reservoirs with the best quality brake fluid ie. DOT 5 in a system designed for DOT3 and destroyed all of the elastomer components. I've had to charge upwards of $800 to replace all of the components in a brake system on a car because of this. 
You may of inherited a problem from a previous owner just because of the wrong fluid being used.
Brake discs can run a little on the hot side. I would drive the bike down the road for maybe 5 miles and coast to a stop. Check the rotors with your finger. It will be warm but should not be hot enough to burn your finger ie. too hot to keep your finger on the disc, but not hot enough to fry your finger with a brief touch.

Thanks scotch and Kawboy!  I'm just trying to work out if mine are too hot or not.    My front discs were only slightly warm but I couldn't keep my finger on the rear disc for more than a couple of seconds. I could possibly fry an egg on it slowly... maybe.  . 

I did use red rubber grease when I rebuilt the caliper, but a very small amount. I haven't had any issue in the past using it on brake calipers. I have destroyed rubber seals in the past with WD40 though, so I now keep that stuff well away from any o rings or seals.

Whoops!  I think it was indeed Dot 5.... I'm in sub Saharan Africa er sorry I mean France,    and I've never found Dot 3 anywhere here. 

Maybe my seal needs replacing then.  I'm tempted to go for a ride and just see how it goes...

I've made a ton of mistakes in all of my years of repairing/rebuilding equipment. My 29 years spent in the nuclear industry taught me many things and I became a better "mechanic" thanks to those experiences. In the nuclear industry, you become more aware of the engineering aspects of equipment and learn to respect proper procedures and why they must be followed to a tee. I started my career as a Millwright apprentice and finished my 29 year career as a Section Manager over Operations, Maintenance, Engineering and Projects. I had 47 people working under me and I became fluent in all of the maintenance trades. At the end of my career I had totaled 703 courses in my training resume'. I share what I know as it relates to our maintenance activities on this site.
Back on topic- There are many forms of elastomers and all have different properties. Some are good for heat, some for cold, some for water related fluid systems, some for oil systems and the list goes on. What you need to remember when rebuilding systems is that the elastomer designed for the system usually is lubricated by the fluid in the system. When rebuilding a system and you need to pre-lubricate the parts to assemble the system or provide primary lubrication before running the system, the best lubricate to choose is the fluid of the system. You really can't go wrong by choosing the system fluid. The only time I would break that rule is if the design engineer of the equipment specified otherwise. In the case of our Kawasaki's, that would be the information provided in the Service Manual which was written by...... Kawasaki Engineers.

I guess a mistake or a cut corner, in the Nuclear industry could be a very dangerous thing for many people and not just ones self or one's bike.     It's great to have your level of expertise focused on these old bikes.
My skill set isn't even in the same galaxy as yours but I always seem to buy bikes from...well... how can I put this... er, very unskilled people... who should probably have their tools confiscated..   I guess it's all relative. . Then again, I'm the idiot who bought it from them.

Anyway I digress, I went for a 300 mile ride today and the brake worked just great! The wheel spins with less drag now as well....phew, job done! Thanks again!