This leads to my suspicion that it is actually the CV joint causing these vibes in some cases ....particularly the ones that are resolved by removing the front shaft .There are a lot of very knowledgeable people here who completely disagree with how you're arriving at your conclusions. Me included. No one here understands your logic, me least of all. The ratios we recommend when running the 42RLE are based on lots of real-world experience on what available ratios work best. You're the first I've ever seen say that things would be worse with 5.13. Worse than what ratio? The factory 3.73? 4.88 that makes the engine lug? I'm not following your logic or reasoning at all and I was never the slowest guy in class.
And I didn' t replace my driveshaft for any reason other than it was cheaper to have Tom Wood provide a new one than to have it rebuilt. It was old enough that I started getting nervous about its CV joint. Having the front CV seize can literally destroy the tcase and it's far better to rebuild the front CV or replace the entire driveshaft before that happens. I was having zero drivetrain vibrations with my 5.38 gears before I replaced the driveshaft and I'm still having drivetrain zero vibrations with my 5.38 gears.