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"I am considering an offer on employment that will take me out of the self employed category. Can I contribute to a SEP IRA and participate in the employers 401k during the transition year?"

Yes. I did it when I made that transition a few years back.
Of course, your SEP contributions are based only on your self employment income and your 401K contributions only on your salary. You have been calculating your SEP contributions figuring you would be paying your own Social Security. Your new employer will start taking Social Security as if you had no income and had made no contributions thus far this year. This change may allow you to put a little more in your SEP and might alter the amount needed for estimated taxes. You can make the adjustment with your September quarterly estimate; or you can increase withholding so you don't have to make a September quarterly estimate.
Congratulations on the new job!
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