[DIYbio] Viewing bacteria on a molecular level, how to do molecular modeling, and seeking beginner guidance

Hi - I am new to biotech (though not to entrepreneurship in general).  I have a whole bunch of DIY questions that I am saving for later - for now I've just been doing a lot of research on my own trying to determine how I want to start and planning everything out.  Any help with the questions below would be greatly appreciated.  

2 - If I were to take the findings from part 1 (and have a detailed view of the bacteria in various states) is it possible to then design a new compound that will accomplish something specific with the bacteria WITHOUT taking existing compounds and without actually doing the lab testing for now?  And what would be the best way to approach this?  Is molecular modeling the best way to go?  Is it reasonable to learn as much as I can about various compounds, etc and then model a new compound from a problem solving approach rather than looking at existing compounds?  (Assume to date all existing compounds tested have failed).  Where should I look to begin learning the basics of how to engineer compounds?  Any links are appreciated.  School is not an option at this point.  I understand the process in general of looking at bacteria, finding targets, then design compound that will achieve goals within parameters - but I'm struggling to find info on how you actually design a compound (without just testing existing compounds for potential matches).    

3 - Is the NYC group I saw here still active?  It would be great to meet with other people from NYC at some point later on.

Thank you so much.  Any other feedback / resources are appreciated as well.