Warped rotor or?..

Grasping at straws here - could a cupped front tire have anything to do with the vibration?
 
Your original post said the vibration was on braking, so its not the tires. Suspension is not likely. Its the rotors, but don't forget it could be the rear rotor. You really need to put a dial indicator on them and check runout. As far as the sandpaper, don't worry about using a coarse grit, it would be pretty hard to actually hurt the metal. If they show visible wear, you also need to measure the thickness and compare to the minimum spec in the service manual. Too thin , they can break.
 
I had some of that uneven pulsing after fitting new front rotors and using the pads that came with them. Despite following the running in instructions they felt grabby. I used some more aggressive pads I had been using with the old rotors, and they solved the proble. I then went back to the normal pads. So some cleaning of the rotors abrasively can help
 
Unless you had a caliper sticking, rode the brakes very hard for a long time like say coming down a mountain, or did some very heavy braking going into corners like a track day on a twisty track, how do you get the rotors hot enough to warp them? If you did none of these things I would start with what you recently did. You changed the fork springs. I've never seen this done on an 1100 but I know when I saw it done on a 1300 a month or so ago in New Jersey the fork tubes were removed. If the forks did not get put back in so they are the same height or some other item was not assembled correctly I am sure you would feel the results more when weight transfers forward as the brakes are applied.
 
Here is how to measure run out :

The magnetic base and dial indicator are available from harbor freight for ~ $20.

Because the front forks are aluminum , you will need a long zip tie, or several connected together . Snug it down so there is no movement .

Put the bike on the center-stand , weight the rear down so the front wheel is off the ground.
Zero the dial indicator and watch the pointer move as you slowly spin the wheel.
 

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I had some of that uneven pulsing after fitting new front rotors and using the pads that came with them. Despite following the running in instructions they felt grabby. I used some more aggressive pads I had been using with the old rotors, and they solved the proble. I then went back to the normal pads. So some cleaning of the rotors abrasively can help

I think some grittier sandpaper may be in my future...
 
I got some 100 grit sandpaper and more brake cleaner and went to town on the rotors and pads. I then took the bike for a spin...

As I said before, when I initially get on the brakes, it is all fine. If I ride along just lightly on the brakes, I don't get any vibrations. When I get on the brakes a little harder, I can start to feel something start to cycle in the suspension. I don't know know how to describe it to say except it feels like it is "up-and-down" and "ka-thunk ka thunk kathunk" lol. I am still wondering if I could have screwed something up while installing the fork springs.
 
Sounds like at least one of the rotors is toast. Again, you need to put a dial indicator on them before spending the money for new rotors. The fronts should be replaced as pairs if either is needed. If you have linked brakes, it could be the rear - but front is the most likely.
 
I did some reading last night after looking at my brake pads. It appears a PO installed sintered HH brake pads, and while I don't know why this didn't happen earlier, lately they have been rusting to the rotors. Of course, every time they do this they strip some of the surface off of the rotor, I thought earlier that the marks they left were just gunk but no such luck. Could this be enough to cause vibration? Still means my rotors are f**ked though...
 
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