Steve, sorry I didn’t get to talk last weekend. Chasing my little guy kept me busier than usual.

Keeping the 1725 and swapping for an Alpine gearbox with overdrive is the easy way. My S3 with a 1600 engine cruises rather well at highway speeds with OD engaged.
I believe a T5 transmission is the preferred gearbox for the V6 conversion. I’m sure you spoke to Mr. Sharkey about his V6 setup. "V6 Jose" Rodriguez is a resource as well.
Here’s a previous thread on the subject that may address some of your concerns.