I belive you are mixing assembling the genome by combining sequences of individual, overlapping inserts of cosmids, fosmids, PACs and BACs (bacterial vectors with human DNA inserts of 40-150kbp) to whole genome shotgun. The inserts of the above bacterial vectors were sequenced using shotgun, but the gaps in the sequence were closed with custom primers.

No, at initial release, the human genome from the NIH side was done by bac-to-bac, not by shotgun.