I did the same as you, removed the entire floor & side panels, & I know exactly how you felt when you saw the bilge rust!
My boat has paving slabs for ballast. I took them all out, dried the floor out, scraped off all the rusty cack & then gave it a paint.
When I put the balast back in I just layed it evenly across the boat. When the floor went down I left a couple of removable pieces at the stern end, water always makes its way to the back, so I could remove any water that might get under there in future.
When I re fitted the boat I just planned it so weight was reasonably well distributed but it is not perfect. To level her up perfectly I have some off cuts of railway line stuffed to one side under the cruiser deck! There was a load of lead slabs under there originally but I weighed them in at the metal merchants.