Hi K.,
Well I think all the things you are going through all coincide together. There are alot of battles that you need to fight and get worked out. In my response I'm gonna try not to sound harsh and mean but I am gonna call it like I see it so here it goes and this might be kind of long.
1st, I think you need a good routine/schedule. I'm a home child care provider and here is our daily routine that we run on everyday.
7:00 am get up get dressed and ready for the day.
7:30 am - 8:00 am breakfast
8:00 am - 9:30 am(You should add in a learning time, either get him some work books or there are some free websites that you can print things off of. This will make him tired and need a good nap :). Have him do this at the table and you can get the dishes done or in the dishwasher.
9:30 am -11:30am morning free time, they can go play in their rooms or whatever. At 11:00 am go start lunch.
11:30 am - 12:00 noon lunch time
12:00 - 12:30, get cleaned up from lunch, you have time to clean up the kitchen from lunch.
12:30 pm - 2:30 pm, nap time and you a nap or a chore or both.
2:30 pm - 3:30 you can do 2 things: A- do somthing more of learning or B- something that is still structured ie, play do, coloring even scissors and a piece of paper. While they are doing this you can get their afternoon snack ready.
3:30 pm - 4:00 pm afternoon snack.
So after snack thier day is over as far as learning things and such and they have the rest of night to play and things.
So from 4:00 pm - 5:00 pm you have some free time, you can accomplish another chore if wanted, sit down before the evening begins.
At 5:00 pm start dinner.
6:00 pm dinner time.
By the time dinner is over it would probably be around 7 pm. So after you get dinner done then you start your nightly routine.
So at 8:00 pm you would do The 4 B'S:
Bath, Bedtime drink then Bed.
So by the time all this is done it should be 9:00 pm. When you lay him down give him a hug and kiss and tell him good night. You should be able to lay him down at nap time and bed time the sameway.
2nd, Now you need to establish some rules and some consequnces. So you and your husband sit down with a piece of paper and list your rules and come up with the consequences to go with them. This way you are both on the same page.
Back each other up when the other parent is disciplining you son.
You shouldn't have a disagreement on the consequence because you have already established these things. To me I see your son has the run of the show. At 3 he is able to run the show in your house, he is YOUR boss not the other way around. If you don't get control of him now it will be so much worse in 2 yrs and then even more worse in 5 yrs and then in 10 yrs when you really want the control it will way to late.
You have alot problem areas that you need to fix, here is what I see:
Bedtime, staying in bed, patting his butt, rocking him.
sippy cup and the amount of time you refill it.
Taking him off whole milk and then onto soy and then the fish oil. You can't expect 2 things that you change to fix all the problems you are having. Specially when some of them are what you are allowing to happen and he knows how far he has to push to get what he wants.
Then sleeping with his shoes on.
Him not listening to you, I'm sorry to say but your 3 yr old has no respect for you as a parent. He sees that no matter how far he goes you will go right with him. He has no boundaries. And if he does you give up to quick.
Then you have the attention. At this point it isn't even about attention. He is able to boss you around and he is 3 yrs old. Kids will do whatever they have to do to get attention wether it is negitive or positive.
So you and your husband need to get a backbone. Get a routine or follow the one I gave you, adjust to your house hold.
Let him know there are new rules, explaing what they are.
Throw out all the sippy cups, in the trash. Let him see you put them in the trash. At 3yrs of age there is no reason he should be taking a sippy cup to bed. This is also giving him more sugar and things like this. Also over the age of 2 they no longer need whole milk and could be moved to 2% or less. Make sure he is eating a well balanced meal everyday and at all meals.
By the way all kds have currency at any and all ages. Find what his currency is and start taking things away and priveleges.
I hope this helps, W.