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question for those who also play guitar.

Any other bassist/guitarists have this problem when staring on guitar?

Nope. Perhaps it's because I started playing guitar a year or two before I started playing bass, but 15 years before I started playing 6-string bass.

But more likely it's because there's this weird paradigm shift that takes place whenever I strap on a guitar or bass: For some reason I am completely at home with whatever instrument I'm playing, to the extent that I almost have no awareness of the other instrument! When I'm playing bass I can read bass clef just fine, but treble clef really screws me up; yet when I'm playing guitar I can read treble clef just fine...and bass clef screws me up! When I'm playing guitar I don't even have to conciously think about the interval difference between the 2nd & 3rd strings; when I'm playing bass I don't even have to conciously think that there isn't an interval difference between strings. I strap on an instrument and I am transformed into that instrumentalist.

It's actually kinda freaky.
 
Yep the tuning on guitar is helpful for chords but cumbersome for scales and rifs.

I disagree. You just have to (re)train your brain. When going from the G to the B, think "up one fret" for the same interval between two strings tuned in fourths. For example, going from E on the G string (9th fret), the G on the B string is at the 8th fret instead of the 7th. Learning all of the notes at every fret on every string helps trememdously.
 
Yep, I have that problem a lot. I used to play guitar exclusively but when I switched to bass, I felt it was a lot easier to play arpeggios and run up the fretboard. When I switched back to guitar, I usually need a few minutes to get used to the different tuning but, after a while, it all comes back. The key is to stay up to date on both instruments. Don't quit one or the other but practice on both.
 
Instead of playing that minor 3rd we've come to know and love with your index, now you play it with your middle finger...

And remember, blues is the only thing you are allowed to play on the 'lead'...no, seriously, that's it.

Shameless plug for Albert Collins (here). Don't try to figure out his tunin' just find the notes!