Thank you for your reply.
Yes, you are right, is is a mess made in a rush... should keep more attention next time to it. However, I have some news. I had some time today and tried to reduce the 100nF cap down to something else. Removing it made the readings more reasonable and replacing it for a 33pF - the only one I have found, solved the issue and now the RPM is showing reasonable values 
If you think it would be beneficial to do the "right" schematics and probably help someone else that would be searching for the solution, I will do it. If you know some online service for drawing these stuff, recommend me something, I have tried several today, a few of them were good ones but before finishing the schematics, they have locked my account with - your trial period is over and thus couldnt finish it.
regards, Tomas