Can't help with a shop, already don't have enough space, but I'm quite familiar with those rusty areas on a 60.
What do you want to see as a final result?
Factory look?
Close to factory but you can tell it's been worked on?
Back yard 5 minute special?
When I did mine (don't have any pics right now) I cut it all out, formed an L shape with 18ga sheet metal, then used a stretcher/shrinker to get the contour. But getting that dimpled in shape over the wheel well is much harder unless you make a die for a roller or have a lot more time to form it. I also got rid of the lip under the wheel well (where the wheel well and outside panel join) since dirt and water alway accumulate there and it rusts out every time.
As for the rear section behind the wheel, again, if you're ok without looking stock, cut it flat. Then weld some sheet metal to cap it and you're done. It's a fairly useless, decorative section anyways.
It takes a bit of work but if you cut about an inch above the rust and replace it with new metal it should last you another 10+ years. Mine still look better than what my friend had "professionally" done at a shop with his.
As for buying stuff, yes, there are some replacement panels (I think 4wheel auto in alberta has some) but they aren't the full panel and depending on how much rust you have it might not work.
Another option is buying some off an FJ out of the US.
There were a couple guys in the Seattle area that were often parting 60. Check craigs for ads in that area.
If I had more room I'd offer the shop but as it stands anything I need to do is a game of tetris.