Projects How would you fix this? Rust holes in weird spaces!

What Blazingangel (and others) said - get as much shape information as you can before any blasting or cutting.
And if you are not an accomplished metal shaper you could always pull moulds for hammerforms in the complicated areas. (I've done it with fibreglass, but even concrete can work). It is tedious, but can yield perfectly shaped parts without years of practice.
A buddy of mine did just that on his late '20's Dodge - pulled from a creek bed in pretty bad shape. He had no sheet metal experience when he started this a couple of years ago....

 

Wow BarryA! That's some killer metalshaping your buddy has done on that early Mopar, and made it into a 2dr. sedan, taboot!

That shows what's possible with a few hand tools and some effort.

 

Yeah - he is a highly skilled wood worker so that helps I guess, but I'm still stoked that I had a hand in getting him started (he wanted a visor for his early 50's 3100 - I told him I didn't have time to make it but would show him how..) He sure puts in the hours though:2-3 hours every night and most Saturdays - not sure how he gets away with it - I pulled that shit for 2 years and it cost me a wife LOL!

Early on he picked up Mindover's DVD - best metal shaping purchase I ever made, I highly recommend it to anyone.

He is also busy on a '32 Plymouth coupe that was in even worse shape than the Dodge! And has complete an impressive restoration on the truck...