Install an aluminum heat shield between exhaust and tub. You can mount it directly to the hat sections, but it will work better and collect less debris with a little stand-off if you have the clearence. I just used 1/16" 5052 aluminum and rolled the edges a little for some rigidity.
As for the cross over pipe, I ran one on my 3B for 20 something years and they do mellow the exhaust somewhat. I used 2 1/4" pipe with a downward canted "nipple" welded into the header collector immediatly in front of the flange and routed the removable U shaped cross over pipe in front of the cross member and above the skid plate. It made greasing the front drive shaft a pain in the butt and was not re-installed when I replaced the headers (Hookers). Worthwhile? Probably not.
1955 CJ 3B, 381" sbc, AGE M22W, Teralows, Warn OD, OBA, Premier Power welder, Warn 8274
1968 CJ 5, factory 225" w/ headers/450 cfm Holley, T86AA, Belleview winch, Warn OD
2012 Wrangler Rubicon Unlimited, Warn 9.5 xp-s winch