As for replacement sills, try Lighthouse (they're in the suppliers section) if they don't do them, they'll know where to get them from - if you can get them! I know people have replaced the whole sills with box section before now.
The sills on a Cherokee are structural as there is no separate chassis. Don't go just riveting something over the rust hole, it needs to be welded up properly.
As for checker plate sill covers, don't think anyone does them, but I'm sure someone local could form some for you so you can hide any untidy welding.