Hi
It sounds like you are trying to work out what works best for your son, and to try and avoid situations that will result in him having a tantrum - it is very understandable. Sometimes when you are in the throes of dealing with challenging behaviour, it may seem an easier option to 'give in' but it is only a short term strategy with potentially no long term benefit.
I think you need to choose 1 or 2 (that are most important to you) issues to begin with & deal with them and progess from there. I think a child crying is a cue/clue that they are in distress. It is often that they are overwhelmed with the new emotions they are experiencing as well as a lack of skills to deal with it.
It also depends on how your child sees the world, it may be that he is visually orientated in trying to interpret his world.
if that is so, planning his routine may work better using pictures as reference for him. In terms of getting dressed, if you have a series of activities that need to be done to get him ready, have a picture for each one, so that he can follow the routine & it gives him more involvement in it also. It may be a longer process initially, but if he buys into it, it will be worth the effort. In relation to who puts the socks on, have only one person involved in helping him to get dressed. Distract & divert away from who does what & encourage more of his involvement. Engrossing him in the process, may help him 'forget' about who is helping him & engage him more in the activity.
In relation to the 'pen' I would remove it or if he is using it, do so under supervision - he was exploring his worlds & a sofa is a canvas for a 3 year old artist!!
If there is something that he's really upset about... wait until he is calm, maybe an hour later or before bed. Tell him how his action made you feel, without laying blame eg, 'I felt irritated when you ....' & request that he tries to do it differently next time.
Watch for trigger events & talk to him in a preventative way asking for the behaviour you desire on the occasion. Bear in mind that behaviour has to be taught, and as with learning anything new, it takes time, repetition & patience. And there has to be lots of room for mistakes...
Maybe talk to the nursery staff & ask if they have any suggestions & also to check how he is most of the time at nursery.
In relation to speaking to your neighbour. I would role model. He will absorb how you are behaving & communicating & learn more from your actions & behaviours than him having to say good morning. Let him watch & learns & he will in his own time say hello also.
Get support for yourself & discuss your plans with those around you. Everyone must be following your strategy.
Tell your son that you love him & that you are going to work together to finds ways to help you to live more peacefully together.
Also it may be nice for your son to see him being prioritized over his younger sibling on occasions..eg OK... I'll be with you (baby) in a moment , I'm just helping... with...
Only a few thought.... best of luck