Avoiding Tweaking Blazer Body??

[Huskerboy2]

I've heard people talk about tweaking the body of their Blazers out of alignment before. What are the dos and donts of replacing body panels and installing patch panels on a Blazer. For example, If I keep the top on my Blazer and keep the tub on the frame, can I pretty much remove any body panel I want to and cut out any rust and weld in new patch panels without worrying?

The main reason I ask is that I've got the top on my Blazer right now and the tub is mounted to the frame. The tailgate, doors, etc. are all off the truck. I need to remove the rear cross sill that runs across the back just under the bed because I have some rot that has happened along the rear of my bed due to moisture being trapped in between the rear sill and the bed. Can I do that without fear of tweaking anything? Do I need to rig up some bracing or anything?

Thanks everybody.