With the installation of my new heat exchangers on the 3.0, I can't align the cone screws so they line up with the holes in the rod. I'm thinking I just need to drill new holes. Anyone else have this issue?

What linkage are you running? Aren’t there splines that can be readjusted to line things up?

Is it the HE's or the 3.0 that are new? The six needs a different shift rod than a four.

I ditched my 911 style coupler for a uni joint because it has a 2way action did the same @ the rear as per what some venders supply but that can only be used with a dual console bushing for best result.
Replacing the conventional firewall coupler is a step ahead with one of TR's bulkhead bushes expect you already know that by now.