Sync Up Your Guitar Hands in 3 Steps

Does your fret hand lag behind your picking hand? Perhaps your picking hand just can't keep up with your fretting hand? In either situation, what can you do to fix this problem? Simple answer - metronome!
I have said this before many times, and I will keep saying it - the metronome is your best friend when it comes to improving at any instrument.
Want speed? Metronome.
Want accuracy? Metronome.
Need to improve a particular rhythm? Metronome.
House on fire? METRONOME!!!
Okay, not really the house on fire part, but I hope you understand how important I feel it is to use that metronome.
Whatever riff you are trying to clean up and get your hands in sync with, you will be using the metronome to help ease you into the higher speeds to achieve the BPM you want.
But, let's say you still don't have this particular riff down very well. If that's the case, the first thing to do is practice without the metronome so you can better focus on the movements of both hands. You're going to have to play SLOW. Probably slower than you think you should. You need to be able to focus on all the movements of the right and left hand. You need to make each motion a very conscious movement. 
Keep playing your riff at a very slow pace until both the left and right hand are perfectly synced up, and you can play the riff repeatedly with no mistakes. Once you can do this, turn on the metronome.
Start at 60 BPM. Yes, just 60. I do this myself and have all my students start this slow. The excuse of it being TOO slow is just that, an excuse. You need to be able to understand what you are playing at slow speeds anyway, so start slow. It's important!
How many notes do you play per click of the metronome? Depends on what you are trying to practice. Common divisions are one, two, three, or four notes per beat. I recommend starting with just 2 notes per beat for most things.
Each time you play your riff correctly, bump up the metronome by only 5 BPM. Anything more than 5 BPM is too much of an increase. You need to let your brain and hands get used to the movements nice and slow. Jumping up to higher speeds too soon will do you no good. It HAS to be slow increments!
Keep bumping up the metronome by no more than 5 BPM each time the riff is played correctly, and only stop doing this when you can't keep up anymore, or you notice you can't tell if you are still synced up. 
When you can't tell if you're synced up anymore, back the metronome up by 10 - 20 BPM. Now, play the riff again at least 10 - 20 times. No stopping in between either. It must be played back to back to back to back until you hit the high number of repetitions. 
Doing a lot of repetitions is what I like to call volume training. I got the idea after reading a comment Roy Marchbank left on his video on how he made his technique bad ass. He is a beast!
Constantly repeating the riff at a pace you are being pushed, but you know it's done correctly, will help pound the movements into your subconscious. Being able to play fast, and synced up, requires you to have the movements in your subconscious and muscle memory. You simply cannot think fast enough to watch every possible movement when you're hauling ass on the fretboard.
Let's recap the 3 steps to syncing up your guitar hands:

1. Keep playing your riff at a very slow pace so you can focus on all the movements of both hands. Do this until it feels comfortable and natural.
2. Turn on your metronome at 60 BPM. When you play the riff along with the metronome correctly, with no mistakes, increase the speed of the metronome by NO MORE than 5 BPM. You can do less, but do not do more. Keep doing this until you can no longer tell if your hands are synced up, or you just can't go any faster.
3. Back the metronome speed off by 10 - 20 BPM. Now play the riff at this speed about 10 - 20 times. Once you can do this, start bumping up the metronome again until you no longer can increase the speed of what you're playing.

That's the process I recommend for getting your hands synced up.