Ok, Oddly enough I got it to work. I tried this method numerous times but it would not work until now.
Since I only saved the 'minecraft' directory, I created a new instance, started it, then stopped it. renamed the 'minecraft' directory in the new instance to 'minecraft.old' and copied the 'minecraft' folder from my old server to the new one. Started the instance and modified some setting including which jar file to use and started the server. It worked
Like I said i did this a few times before and it did not work. Remains to be seen if any anomalies occur but for now I am happy.