It all depends on how well the clear sets up. If it's hard enough to sand without gumming up the paper in a two or three days, and if it were me trying to save what I could rather than starting all over again, I'd make certain it's hard all the way through before trying to knock down the heavy stuff.
You used a hardener in the clear didn't you?
By the way, you'll need some thing a bit more aggressive than 1000 grit to sand those runs down at first. I'm thinking 320 used 'wet' on the heavy stuff, then you can work your way on up the grit scale when you get the high spots knocked down. It all depends on how much clear is over the base and how the defects look.
Personally, I'd strip the tank and start over. Sorry..
How about a few more pictures now that everything has had a chance to settle down a bit.
You used a hardener in the clear didn't you?
By the way, you'll need some thing a bit more aggressive than 1000 grit to sand those runs down at first. I'm thinking 320 used 'wet' on the heavy stuff, then you can work your way on up the grit scale when you get the high spots knocked down. It all depends on how much clear is over the base and how the defects look.
Personally, I'd strip the tank and start over. Sorry..
How about a few more pictures now that everything has had a chance to settle down a bit.

