Due to a variety of problems with the current implementation i started to refactor the spot functionality to poll the spot instance request for the instanceid until its known.
From that point on the Spot instance can be treated as a regular OnDemand instance.
I am currently testing the functionality on our system but will create a pull request once its working for a while. (Please have a look at https://github.com/nexus49/ec2-plugin) in case you want to provide feedback.
With this functionality it is not necessary to do any modification on the used ami specifically for spot support.