Like what everyone else said, keep eating and you will fill in.
But as for those problems areas, heavy - closer than shoulder grip smith machine shrugs, in front of your body, HEAVY! Dont bother with any variations, just stick with those..
I get very good separation in my upper pec/ between my traps and delts by doing smith machine presses on a degree more than incline bench, but less than military. Keeping the grip just outside of shoulder width. Stay in the 8 rep range.
Squeeze the shhhhit out of your traps n pecs at the top of each rep
Lighten up man. No need to be a dick. If you haven't, at some point, had to resort to liquids to get the calories down, then I'm going to question exactly how much mass you've added to your frame over the years. Your profile says you are 5'10" and 180...so it kind of sounds like you are parroting some author.
Waylander is one of the biggest motherfuckers here and he drinks like 75% of his food. Does this mean that whole foods aren't the BEST choice? Of course not, but 5000 calories of liquids AND whole foods is going to go a lot further towards building mass than 2000 calories of just whole foods.
Well..the chipotle burrito is ~1000 calories and the weight gainer is ~1000 calories per serving...so yeah...it's definitely feasible that he might be hitting 4000-5000 calories a day.
OP, stick with it. This shit takes time. Measure your progress in MONTHS and YEARS, not days and weeks. If you gain 15-20 lbs a year, you will be 75-100 lbs heavier in 5 years time. Stick with it and be consistent.