I always mount the engine in the mounts first, then mount the mount to the firewall...Is this an ARF?
Once you have the proper spacing for the cowl is there play in the engine at the aft of the mount? if not drill those first and secure the aft side first. before you drill the forward holes
make sure that you have enough area on the mount to drill the forward holes without drilling through the side of the mount. if its close re mount the mount on the firewall.