I am looking for a clean sound from my clapton strat. I dialed up to 9 on volume and put it through a 65' twin reverb reissue at 2, bright, no reverb or vibrato. I was surprised at the level of distortion. I always pushed the amp to get to that level.

Is this normal or do I have a PU problem?

No. It's completely normal. If I play to hard on my Clapton Strat it will distort my Peavey Delta Blues on the clean chanel. I would dial back the volume on the guitar.

In my experience Fender amps always seem to go from 1-2 too quiet to 3 or high too loud.

From what I know about Clapton's playing, he doesn't use any effects, just strait amp volume and the guitar.

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1975 Sunburst Stratocaster rosewood finger board
1979 Stratocaster with roseowood finder board
2001 Candy Green Clapton Stratocaster
2007 Andy Summers Inspired Telecaster
2007 '51 P-Bass
2012 Taylor 110
2015 Mystic Ice Blue Deluxe Stratocaster Plus