DDR and DDR2 as a main memory

Sorry for the delayed response, been busy.

From my experience, when it fails to pause the processor, I either have a reset incorrect or a clock that is not running, thus it never comes out of reset.

I agree with BadOmen, start small and work your way up. Not just with the IDE and procramm running, but the whole SOPC project. You said on the DDR board you have an example design working, start from that and add DDR but still run the program out of internal mem, then try and run it from DDR, and see if you can make that process work. For the DDR2 board, if you found your error with the DDR board then work from that, else start the same basic process over.

Make use of signaltap need be. You can route all of your clocks and resets to it, then you will know if everything is up and running or not.

@BadOmen, the rup and rdn do not require connectivity to use OCT i don't believe, only if you want to use calibrated OCT. You can use uncalibrated OCT without those connections, although it is less desirable. Correct me if I am wrong though.