100 ps? pfffffrt. 10 ps, yeah that's the tricky part of the 10-100 ps range.
I didn't use an MMCM for delay compensation, but maybe you come up with something clever. So don't let my opinion get in the way of progress! Try it and let us know what works and what doesn't.
As for simulation ... expect pain. XD You'll have to do post place & route simulation and long runs to get something useful. Also, run it in real hardware with some nice bandlimited white noise on the input, capture your TDC outputs, collect all those TDC outputs in a large file and do something clever.
Preventing optimization: lots of KEEP and SAVE attributes. Also, see the xilinx constraints guide.
And I noticed in the latest paper that they upped their game, the b4stards!
Now I will have to get me one of those parallella boards and set aside a few weeks coming winter to see if I can do better.
Do you happen to know how the ZYNQ-7010 carry chains compare to that of a spartan-6? And on the subject of specific fpga's, what fpga are you implementing this on? Virtex-6, or something even more expensive?