Hey Chinmay,
I am sorry for a long response time. I was caught up in some other work.
The problem in your log is saying that there is no IDELAYE2 module even though you have in instance of IDELAYCTRL module.
These modules are instantiated in chipset.v and I can't imagine any situation when one is instantiated without another. So you probably had either logic modifications or synthesis/implementation results which were used from previous runs.
I implemented system on vc707 using protosyn -b vc707 -d system --uart-dmw ddr command without any troubles.
Can you try do it on a clean repo and tell me if you still have any problems?
Best,
Alexey