Thank you for your reply!
I have also come to the conclusion that a PUF based on wire delays is not suited for the CAD/FPGA environment. I am therefore going to try and implement an Oscillator Ring (OR) PUF, or an SRAM PUF instead.
For a good explanation, please take a look at Figure 1 of this paper:
physical unclonable functions for device authentication and secret key generation (
http://videos.dac.com/44th/papers/1_3.pdf)
Figure 2 shows the Oscillator based PUF. Do you think an RO PUF would work better in the environment I'm working under?
Thanks!