Maybe stop worrying about it? Seriously. If you can do 50 pushups in a month do you think should should be able to do 100 in 1 month and 2 days? When you are ready the world provides. It seems you are not ready. No matter what I say(or anyone else) there is something that prevents you from doing it and it is something unrelated to technique. That is, you have other problems and the universe is saying "Nope, can't pass go... pay the fee".
I had the same problems as you... I worked on it too. I got better but always had problems... then I stopped trying and just started focusing on music. Everything comes when needed. I no longer have picking problems because of time and practice.
See, there are a million techniques. Can you rasgueado? What about strum any rhythm? Can you sweep pick well? Do you know all your arps and chord shapes? What about modes?
So much to learn. If you focus only on one thing you never get anywhere. I do get the reason why you do this, it seems natural; It isn't.
Thinks take time to happen. We always want it all now(specially in the modern era where we have to constantly compete with the best of the best since everyone expects everyone to be the best or they suck).
You will improve 10 fold if you just focus on music. Maybe you were not meant to alternate pick fast.
I will tell you though that it is likely you are doing it wrong and it is very likely you neglected other techniques in your pursuit to "master" a single technique and this actually has slowed you down(again, it seems backwards because we think if we just continue to hack away we will eventually get it and we likely really want to do it and don't care too much about the other stuff). But this is now how to works.
I do not know your exact problem because you were not clear. Likely you do not know your exact problem either.
I can say from my experience that I could alternate pick too and learned relatively quickly(it is not a hard technique). I will also say that your alternate picking is probably not as good as you think(better than most but not as close as good as the best).
Sweep picking is critical technique in fast alternate picking and string skipping. Knowing some math also is necessary. You cannot alternate pick everything. All the fast alternate picking stuff done by "shredders" is highly calculated in some sense.
What you mean by going out of sync is vague.
This is how you alternate pick: Every single string set of notes has to end up on a stroke that lets you "sweep" to the next string. This technique seems very awkward but is necessary to have fast and smooth alternate picking. Hence if you never practice sweep picking this likely will cause your alternate picking to be dysfunctional when used over multiple strings. Because alternate picking is binary(up down) one has to match the number of notes played to the direction they are moving to the next string.
E.g., if you have 3 notes played and are moving to the next lower(ground) string then you have | up down up ^ down up ...| but are trying to go up while also having to move the hand down. This is easy slow. It is reckless fast and will take too much time to move which causes issues in timing.
In this case it | down up down ^ up down ... | This is better but now we are going down while changing but we have to overshoot the 2nd string to come back up. This is also easy slow(and should be practiced). I have gotten quite fast as this and I almost always use this method except at the fastest speeds. This is just straight alternate picking.
| up down up ^ up down ... | Try that, that is even more awkward. You can do it though and sometimes it is necessary to change the order to get things to work out later
| down up down ^ down up ... | This is the correct way. The down ^ down is simply a sweeping motion and is most efficient since there is no change of directions of the pick for both strings. Hence it is theoretically as fast as strumming.
You can see though that if you play 2 notes everything has to flip: | down up ^ down ... | and |down up ^ up | fails(2nd one works if you are going the opposite direction to a higher(ground) string).
But here you have to start the with an up stroke so your next note is down | up down ^ down| then continue with a down stroke. You see though this causes problems when you are string to go through multiple strings:
| up down ^ down up ^ ???? | and when we get to the 3rd string we are screwed again.
This is why all those flashy runs are specifically designed to work so one can sweep every motion between adjacent strings. This requires one to choose the correct number of notes per string so it all works out.
This is not difficult but it takes some practice to get a feel for this so you can actually do it naturally.
Again, there is no quick trick. There are many little things involved. If you simply practice music and playing it all comes naturally, is more fun(less boring practice) and you'll be well rounded.
It will happen. Learn from others and don't focus too much on the specifics(you can, even intensely, but don't focus on it for very long). Just know that "I have to pay attention to the notes or it won't come out right. I have to sweep between strings because that is obviously the fastest way. This means how many notes I play matter". If you truly understand the basic ideas that make you have to choose certain number of notes per string, what direction you start with, etc. Then OVER TIME your mind will figure it out as you practice doing similar things(e.g., if you are working on a song or lick or improvising).
You cannot learn to run before you can walk. The universe won't allow it(well, it will but it will make you fall on your face in the process).
It is a key idea in getting good. To recognize the process of learning and that there is no "single technique" that matters. All those fast players simply got fast by playing. They didn't really focus on anything specific. They focused on doing what they wanted(e.g., certain styles or sounds or feelings) and those techniques then progressed. In some sense the less you focus on the specifics the faster you will learn(again, this doesn't mean not to have any clue, it means that you don't spend all(or even most) your time trying to perfect one thing after another.
I will say that you will get better at it with general practice(which includes playing fast alternating and sweeping licks in musical contexts). In some sense, it's like some trick the universe plays on you. The more you focus on X the more it keeps it from you. (it's not like this in reality but it's the same if you try to learn steps in isolation. The reason why you can't take a step is because your trying to use it to run rather than walk like the universe wants you to do. It will let you run only when you want to run for the right reasons and have done enough walking)
EDIT: I can actually do this sometimes but can't pull it off without hitting the lower E as long as the others.
