PCIe as Soft-IP via CMU as transceiver in Stratix-IV

You're probably out of luck here. The problem with the CMU channels is that they don't have the PCS layer. Most soft IP vendors for FPGAs that have PCIe cores require a PIPE interface to the transceiver. I don't know if anything has changed in the last year, but last I checked, no one had the PIPE PCS done in soft logic. I also don't know if the CMU channels have the logic to do link detection that's required by PCIe (they might). You're better off moving one of the other channels to the CMU and using a full channel for the PCIe.