Yes i took off my guitars neck and found some not pleasent dings at the end of the neck (two to be exact). They are very small but could this have on effect on the guitars tone and resonance. Am i just obsessing or what?
You're just obsessing, if anything the only thing that's going to have an effect on the guitar is you messing about and taking the neck off.
No, two tiny dents won't have an effect. Just put your neck back on and be sure to tighten it down well, generally you shouldn't disassemble your guitar for the hell of it lol.