The reason that free weight is hard is because you are incorporating your stabilizer muscles. If you are using the machine then you don't have to stabilize it. The machine is doing that for you. If you really want to get difficult try using dumbbells instead of the bar.
As for your shoulders feeling the burn more. They will burn. A common problem with people who bench is torn rotator cuffs. Try moving the bar to right across your nipples on the negative. It will make a slight arc to be roughly between your shoulder and chin on the extension. You may have to lower the weight and get muscle memory down, but that's where you need to be.
That being said, bench press is more statistical. It will help your chest development, but dumbbell flies, dumbbell press, dips, etc.. will help with your chest size more. People are different. You will need to find what works best for you. Stick with it for 3 to 6 months and then change. If you don't change your workout your body will get in a routine and stop growing.
If you read anything to do with bodybuilding they recommend casein/whey mix before bed with green leafy veggies. i.e. spinach, greens, etc.. As long as it's clean protein it shouldn't increase your body fat.
When I was eating cleaner I had about 40 to 60 grams of whey/casein before going to bed and still lost weight.
My wife had her gallbladder removed after our last kid about 9 years ago. One thing I will warn you about is you may find that certain foods flow through you. It doesn't seem to work the same on everyone, but many people definitely have to change their diets. I've heard some doctors tell her "no that doesn't happen" then plenty of other doctors say "it's very common".
Another thing is it can cause you to gain some weight. If you stay on it, it shouldn't be a problem, but again each person is different.