I think a lot of people had the same feeling about the contract...the moment Bradford yeeted Donald, the contract was null and void. I think they just opted to give Louie a moment and circle back to the whole message that family is the greatest adventure since the series has always been about that.
As for the whole cloning thing, it was a bit unexplained. The stone of what was combines two things into something new and the only thing I could think of that makes any sense is that if two animals touch the stone it creates a freaky hybrid of a similar age between the two. However, if you provide the stone with the genetic material of two animals, it combines them but it doesn't have enough "information" to make an exact clone, and the result is a de-aged new product. I can only rationalize this with the ButterBear being in a cocoon...maybe the wind blew the hair of a bear and the chrysalis of a butterfly onto the stone and it made a ButterBear larva. In Webby's case for being cloned, after Scrooge made the Papyrus only appear to his descendant, Bradford knew he needed to somehow make a clone. I am guessing he took a feather from scrooge but it is unclear if he used another feather (Maybe from Pepper?) to combine it to make a baby Webby/April since Finches journal said "What was once TWO becomes anew". If he used two of Scrooges feathers, it would just make another Scrooge. As far as May and June, they were made from Webby's feathers as per the document that Webby found/read in the archives.
Speaking of May and June, I kind of agree with what's been said already which is it sucks they didn't leave breadcrumbs for May and June in previous episodes, however I can understand why. People already had apparently figured out that Webby was April some time ago when the characters were leaked and there was a voice cast list for May and June, but not April. They may have gotten around this by introducing them early on under a different name having May and June switch off and assume the personality of one character which would have been a better payoff. The only downside is this would just end up as Lena 2.0 more so than it already was, and better to just have it at the end of the season since this was Bradfords backup plan.