Hey Tony,
Try this... turn on the X2 metronome during playback, and SOLO the drums. See if the drums are keeping perfect time with the metronome. If not, try to fix the off-time measures. If you don't get your "pulse" right, the strumming will never match except by luck....(or you know exactly where the mis-timed drumming is.)
Then, Mute the drums, Solo the guitar, and see if the strums are in time with the metronome. If not, check the location of the mis-timing, and see if it's the same places as the drums were. This step is just a check.
Once the drums are keeping time with Sonar (and I really don't think Sonar moves the tempo around unless there are tempo changes in the tune), you MAY need to re-record your guitar part, depending on how far off it is. I honestly have good luck with Audiosnap on rhythmic pieces but NOT melodic phrases. Maybe I just don't know how to use it properly yet... But it hasn't worked well for me. I generally have much better luck by analyzing my wave, trimming the mis-timed parts, and moving those trimmed clips back or forth to fit, either manually or by using Nudge.
Check your Event List just to be sure Logic Pro didn't insert some tempo changes into your song. Take them out if you find anything unwanted.
I'll take another listen to your song shortly. Take care.