Yep, know it well as I had the same experience on the EX-5 but after a while it becomes second nature as everything is in uniform patterns up and down the fret board. I find it best when playing around 5th fret as you don't have to play an open low E as it is right there on the 5th of the low B. Notes lower than D on that string are very dark and I don't seem to go there.
After a while I get lost in where I am on the fret board as you tend to play by ear after a while and everything just seems to fall into place. Really weird when you first jump back on a 4 stringer as you have to recalibrate your brain a bit.







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