Complete 4 speed install with rods and shifter

I have been a manual trans guy since 1970. I have done a couple of conversions.
I have stared at your pics for 10 minutes and I just can't see what's going on. :(
Is that a custom shifter adapter plate? It looks about double-wide to me ........
And are those custom rods? I cannot remember ever seeing rods offset to the driver side that far.

I humbly suggest to remove the entire shifter mechanism, mount the engine and trans, and then go back to the shifter. I would mount the crossmember first, then drop the engine onto the mounts. This will tell you if the brackets are correctly installed onto the engine lugs.
And yes IIRC the crossmember only fits one way,
And yes when done, the engine and trans should be offset to the passenger side about 1inch.