I picked up a kill quest to assassinate a man in the Valtheim keep, but all i can find it the Valtheim towers
which i cleared a long time ago. But i wen't there to see if it had respawn for my quest, which it hadn't.

So where is the Valtheim keep located?.

I also have a quest to return some ownership papers for a horse, and some money which i stole from
a satchel in the basemant of a house. "Promises to Keep" questline. But i have spoken to Maven and
i told her that i was hired to steal Frost, the horse. But i cannot find the guy in prison anymore, he who
gave me the quest.

1. Valtheim Keep and Towers are the same place. Who gave you the quest? If it's a radiant bounty quest, it shouldn't lead to to a cleared location, but if it somehow did, then you might need to wait until the Towers respawn.
UESP mentions another possibility - Striking the Heart quest from Aela. It says this makes the quest impossible to complete and there are no workarounds. Possibly an earlier save? Unless someone comes up with a solution.

2. After you talk to Sibbi for the first time and get the quest, you don't need to return to him. You have already stolen the horse and the papers, right? So all you need to do now is find Louis Letrush - he's waiting a little bit north of Black-Briar Lodge. It doesn't matter that you've spoken to Maven before - she tells you to go on with the plan anyway. And in fact, after you give (or not) Frost to Louis, she has her own way of dealing with the thief

What is her way of dealing with Louis? She clones him and then condemns the triples to stand in front of the Whiterun stables for all eternity? hahahahahaha

Well technically she's supposed to send a thug after him. But I think spending eternity half buried in the ground might be worse fate than death