I thought I heard that two doctors cleared him and one was from the Colts, but maybe I didn't hear that correctly.
I heard two as well, one was the doctor that did the surgery and the other is unknown.
This is the doctor that performed his neck surgery. I think I'll trust a renowned neck surgeon on the condition of Manning's neck over some random sports doctor who has probably never performed complicated neck surgery in his entire life.
That's the thing though, the only opinion that counts is the Colts' team physicians. If they don't pass him on a physical then he is officially unable to play. The player does not get a second opinion. The Colts team doctors also don't have to give him a pass/fail on his neck, they can give him a pass/fail on anything they want if they want to keep him away.
When Favre was traded to the Packers the team doctors wanted to fail him and void the trade but Ron Wolf overruled them and he "miraculously" passed his physical.
In 2004 the Packers tried to trade Jamal Reynolds to the Colts, the Colts had second thoughts, and Reynolds "mysteriously" failed his physical. The trade was voided and the Packers cut him. He was picked up by the Browns a few days later and "miraculously" passed his physical.
In 2006 Lee Suggs passed a Cleveland physical, was traded to the Jets, failed a Jets physical, was returned to Cleveland and cut, then passed a Miami physical all in a span of about 30 days.
In 2006 passed a Broncos physical, was traded to the Cowboys, then failed the Dallas physical and was sent back.