Nice project! I've used Crosslink-NX and Cypress FX-3 on various MIPI camera projects as well. Did you notice that Radiant does not control the timing of the data from the mixel hardmacro to your FPGA logic? (click on one of the pins in the physical viewer to see this). I ended up adding a ring of flip-flops and physically locking them near the top edge of chip to get consistent timing.

Looking at code: why are you not using the byte aligner built into the hardmacro?