Pretty sure re gearing both ends is a given! what size tires you running or planning on running? What driving do you mostly do? 33" 4:10 or 4:56....35" 4:45 or 4:88 Looking about $800-$1000 to swap so pick the gears that best suit your current and future driving needs.
Axleboy in Stl is a very reputable shop. Others are Pezz performance, first capital 4x4, hellbent performance, craven performance
I thought the same thing when I heard the name. But that's all he does is rear ends. Mostly for other shops who just tack on more money and do nothing.
Got another quote for $1600 at a diesel performance shop. But he was saying maybe some extra charge for gaskets and what not. I hate when they say that, usually means I'm gonna stick it to ya in the end.
You could try to find some used axles. Standard gearing for a SE with the 5 spd is 4.10. They would be a direct bolt-in and you would have a spare set of axles to boot. Check out car-parts.com looks like there's a few close to you.