Went through a similar discovery a few weeks ago. Recorded myself playing over a song, being off doesn't begin to describe it lol. The things a bass break can do to your sense of time...
After two weeks of shedding with a metronome and recording again, it was a difference of night and day, as they say.
Actually recording yourself is the most brutal but honest way you could ever break it to yourself that you need to shed. So taking that step alone is enlightening and your first step to growing as a player.
For me it helped to discard tapping my foot also, and instead going with feeling the pulse of the music in my spine. Whether you bob your head or move your upper body, doesn't quite matter. But I found that I keep time better that way as now rhythm is more of a physical sensation not unlike dancing. Kudos to victor wooten for that (he mentions it very briefly in his groove workshop dvd but the devil is in the details apparently!)
Practicing with a metronome on really really slow tempos also does wonders... Set it to 35 bpm and practice quarter notes. The result may surprise you lol.
In my rcording endeavours I find that I have a natural tendency to be slightly behind the beat, though it sounds like I'm dead on to me. Another thing to keep in mind, I like it that way, the important thing imo is consistency, so stick to what comes naturally.
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