Kerry lost completely on his own merits. The problem with the Swifters is that in questioning JFK, they were also calling into question the service of all the men on those boats during the particular operation in question. That wouldn't have made Bush look good, no matter what the real story was. And the temptation to question anybody's military service in the future will be too great - I'm uncomfortable going down that road (that tactic backfired somewhat with Paul Hackett).
And, let's be candid -- it was difficult for the Bush campaign to comment negatively on Kerry's Vietnam experience when Bush's own Na. Guard service was under suspicion. By not bashing Kerry, Bush could take the high ground, and people would consider the Dems' criticism of Bush's Guard duty petty.