Yes, this was an issue. I was depending (stretching) the idea of a very slow pulse due to the hypothermia (http://www.hypothermia.org/protocol.htm) and that Lestrade and John didn't wait for a long time to find a pulse, John concentrating on warming just in case. He thought he felt a pulse when he was removing the sleeve, but then couldn't find it again. That seems moderately plausible. Once Sherlock is leaning on him, he doesn't take the pulse again, he's drying the hair and rubbing the chest through the towel which is thick. I thought the questions of whether he would feel a heartbeat or respiration through the back was more an issue, but John hasn't taken his jacket off although the sitting room was hot, he quickly joined the others in the kitchen by the open freezer, so I thought a few layers of clothing would be enough to mask a very slow/low pulse and respiration rate. The time John has Sherlock leaning against him is also short. It only takes Lestrade a couple minutes to fetch the towels and then there is the distraction of him realising that the body is Sherlock's. So I had the first obvious respiration and the sound coming simultaneously to John's attention.

So...unconsciousness, hypothermia, impatience (with the pulse taking), short time lapse, layers of clothing and distraction are my main excuses and a disinclination on John's part to eliminate the hope that Sherlock might still be alive.

Too big a stretch?

Would rearranging this bit improve the situation?

There’s a vibration under his hand. John’s fingers dig in. A movement against his cheek.