Hi,
first of all, apologies if I use the wrong terminology at times: I'm new to bicycling.

I have a Marin Fairfax with Sora derailleurs and shifters. I have 3 problems with it (in order of severity):

1. When I'm in the second cog in the front derailleur, and in a cog smaller than the 4th in the rear one, the chain touches the front derailleur producing an annoying noise. The noise is increased if I do a heavy pedalling stroke with my right foot. I have made sure the derailleur is aligned to the 1st and 3rd cogs fine, by tuning the limit screws. How do I fix this problem? I have also tried to change the tension of the cable that runs from the shifter to the derailleur, by removing it from the derailleur side, shifting to the leftmost front and read cogs, and trying different initial tension: it took me a lot of trial and error to even get a setup that will allow me to shift to all 3 cogs, so I'm really afraid to tune that further.
2. Shifting from a smaller to a larger cog in the front derailleur is really hard on my thumb. I have tried tuning the tension of the cable that runs from the shifter to the derailleur, but that will mess up the alignment between the derailleur and the cogs. Any solution or is Sora just that bad?
3. When I'm in the 2nd cog of the front derailleur, and in the 5th smallest cog in the rear deraileur, one tooth of the 3rd cog of the front derailleur will grab one of the links in the chain, lift it just a little bit, but not enought for it to make the chain shift to the 3rd cog. Infact, the link is not grabbed from the inside of it, but from the side, where one of the link's components protudes slightly. That tooth in the cog doesn't seem to be bent.

Thanks in advance for the help!