Damn. All that work and they didnt backflush the welds.
"Most" of it could be cleaned up with electrical acid passivation. If you know of a welding shop that does a lot of stainless, and has the tool for weld passivation, you might ask what they would charge to clean them up. That will remove 80 to 90% of the discoloration and stop some of it from rusting over time. It will not fill in the areas that are capable of harboring bacteria. Some areas could be fused/reflowed by a competent tig welder, but it wont be perfect.
If it's an extremely good price it might be worth it. But be OCD with cleaning and sanitizing.