Granting the higher HD is no problem. It's only an extra 2 HP at 1st level and 1 additional HP each level thereafter (assuming you don't roll for it). Considering you can spend a feat to take Tough and get even more HP than that... giving Monks a small HP boost does not unbalancing anything.
Raising the Martial arts die could be fine-- most Monks use a higher-damage weapon and then the MA die for the off-hand (and flurry) so I've never seen the d4 be an issue personally, but for you it could be different. Personally, I just reduce my duration of Short Rests from 1 Hour to 10 Minutes, and that bumps Monks (and Fighters and Warlocks) up all I need. While the group pauses so that the Wizard could prep a Ritual, the other three are using those 10 minutes to take a Short Rest and get back their class features. That solved my problems easily.
Changing the AC generation? I personally wouldn't do what you proposed. Adding to the Ki pool? The 10 Minute Short Rest solved that issue for me. The extra Skill proficiency? Sure, if it seemed like the Monk character was missing something. A whole heap of subclasses give out bonus weapon, armor, tool, and/or skill proficiencies all over the place... so giving the Monk another one won't be an issue either in my opinion.