Auto to manual conversion. If you could do it over....regrets, pitfalls, long term opinions???

Yep I'm having a linkage problem and a want to work on it problem. Been sitting in garage for over 3 years. It had 340 w/2:94 and it shook so bad the interior screws were falling out. Now has a 408 w/3:23 sure grip and it's better lol. To many cars to work on not enough time. I appreciate the feedback you guys are great. Dustin