The $2.5k per side is close to what I've had informally quoted when I've asked about rockers too.
A lot of places told me they won't even do it because they warranty the body work, and they aren't willing to warranty spots with high rust potential.
You can get panels for relatively cheap -
1996-2001Toyota 4 Runner Body Panels
It's the time and tooling required that's kept me from considering it so far. I would expect at least 10+ hours per side for someone that knows what they're doing. I figure if I try to tackle it I would need to at least triple that time estimate.