INA 203(b)(2)(B)(ii)(II) only excludes work while in J non-immigrant status.....
"....worked full time as a physician for an aggregate of 5 years (not including the time served in the status of an alien described in section 101(a)(15)(J)),...."
However,..... it later says:
(III) Nothing in this subparagraph may be construed to prevent the filing of a petition with the Secretary of Homeland Security for classification under section 204(a) , or the filing of an application for adjustment of status under section 245, by an alien physician described in subclause (I) prior to the date by which such alien physician has completed the service described in subclause (II).
See also 8 CFR 204.12
http://ecfr.gpoaccess.gov/cgi/t/text....1.1.12&idno=8
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