Alright so for a couple weeks I've been having problems switching between positions (only doing the 5 minor pentatonic positions) when a backtracking changes keys. I can go up and down every position, up one then down another one, random direction changes etc.

However what I cant do is switch in the middle of any 2 positions. For example if the back tracking starts in the key of A then I start playing one of the positions over A, but when the back track switches to the key of D it takes me a few seconds (more like 3-5) to find the next/closest note in a different position for D. Sorry if that doesn't make sense, I'll try and make it more clear if you don't understand.

Some people said that I don't know the scales and the positions well enough and to keep practicing and it'll come eventually. However I don't know what else I can do to practice the scales and positions to be able to switch smoothly between them. Recently I've been using http://www.justinguitar.com/en/SC-010-ScalePractice.php and http://www.justinguitar.com/en/SC-012-PatternStudies.php but haven't seen any improvements yet. Some also said I should just start memorizing the entire fretboard a little bit at a time, and once I have that down then apparently it will make my problem nonexistent. Any suggestions? Should I keep doing what I'm doing now, and will it come eventually?
I think what the people mean is just keep doing what you are doing and eventually over time you will get better at changing the positions.

things like this rarely happen over night try not to worry.
Stop thinking about the patterns.

Instead start listening to the scale and familiarise with the notes and the sounds they make. When you're playing you sahould never be thinking "Where's my next pattern?", you should be thinking "Where's my next sound". If you can't identify where sounds are going to come from, and a lot of players can't, then that's what you need to be working on - associating the physical actions and position on the guitar with the sound that comes out. That's why you need to know your intervals, most players won't be able to call out the pitch of every note on their fretboard, but they will know what note they'll get when they move to a certain point from the note they're on. As long as you can figure out the sound you'll get relative to your current note you can get around no problem.

Remember, you don't want to play the scale, you want to use it to create something. Focus more on what sound you want to create, not where to put your fingers.
Actually called Mark!

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i wanna see a clip of a recto buying some groceries.

So are you saying that I should focus more on memorizing the fretboard, and then work on trying to instantly know which note is which as soon as my finger lands on it?

I don't know anything about intervals, but im guessing that's the WWHWWWH thing or is it something else?