What evidence are you using for the arrival date?
Using General Lee's report, most of the Army of Northern Virginia remained near Winchester until early November 1862. Revising my earlier post, clearly Manassas Junction and the rail lines nearby were in Federal hands during the period under review, and not in running order.
Confederate rail communications must have run from Gordonsville, Charlottesville and Staunton. From there take the Valley Pike north to Mount Jackson and on to Winchester.
http://ebooks.library.cornell.edu/cgi/t/text/pageviewer-idx?c=moawar;cc=moawar;q1=Manassas;rgn=full%20text;idno=waro0028;didno=waro0028;view=image;seq=0102
http://ebooks.library.cornell.edu/cgi/t/text/pageviewer-idx?c=moawar;cc=moawar;q1=Manassas;rgn=full%20text;idno=waro0028;didno=waro0028;view=image;seq=0342
http://ebooks.library.cornell.edu/cgi/t/text/pageviewer-idx?c=moawar;cc=moawar;q1=Manassas;rgn=full%20text;idno=waro0028;didno=waro0028;view=image;seq=0389