I can economy pick at about 100bpm, but my problem is the upstrokes and down strokes following themselves (as it changing strings). Does anyone know what i can do to clean this up?

practice slowly with a metronome and then once youre comfortable there push past your limit then stop. next time you practice go a little faster on each setting until youre comfortable.
My Gear:
Gibson Faded Flying V
"Dante's Inferno" Iceman
Fender Hot Rod Deluxe 112

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try practicing stff like the cowboys from hell intro, things that need economy picking, and just practice, it really does help
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Since when can you not alt. pick the cowboys from hell intro?

Even though I'm generally an economy picker, I find that riff really is much, much easier to do with strict alternate picking.

If you want to practice economy picking, just take some general 3nps runs that you'd use to work on alternate picking and just economy pick; pay careful attention to the stroke direction and you'll be good.