Ya, I had to hack my exhaust for the flip, but my exhaust is junk. I've never run a 6" block, I've run a few 4" and never had any issues and they rode/drove fine. I would just try the easy stuff first. Grease all the shackles to get everything moving and in unison. Get new shocks and maybe let some air out of the tires. I don't like my Sky(crap)Jacker softrides, too soft for me. I like my suspension a bit stiffer. The comment on the seat above, yes, you need a good sprung seat. I love the springs in my seat!
It's truck, it has an old carriage type suspension, love it! But I guess you know this and are hoping to mitigate. Keep on truckin!
Oh, look! Here's a hack with some skyjacker softride springs, bet it rides great! Bessy the mule complains no matter what though. And... I did to just get that pick out of the crapjacker catalog!