The signing keys are all contained in the files C:\Program Files\Research In Motion\BlackBerry JDE X.X.X\bin\sigtool.* if you installed your JDE in the standard location.
For applications to run in the simulator the JDE copies over the cod, csl, cso, debug and jar files to C:\Program Files\Research In Motion\BlackBerry JDE X.X.X\simulator (again the default location). I don't know which ones are required, but have a look for the corresponding files of your application there. If they are missing it could be because the eclipse plugin isn't getting them over there when the simulator starts. I don't use eclipse so can't offer any more help.
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