In all of the pictures I have seen, including the latest your engine (to me) looks like it is in crooked. This and the way your shifter sits in the hole all tell me it is not in straight. The shifter should not be at an angle, it should be relatively centered in the shifter hole. In my opinion something isn't right, and it does not seem the new motor mounts corrected this.
Chris
Chris

the cross member I have looks like it can be installed both ways but appears to also move the trans mount location forward or back, he needs to look at his engine mounts to see if there are installed with R/L and not two R or two L mounts.