1) Good question! Maybe it didn't work at the time? Since he was using the ship and all? Pure fanwank, that, but he might've picked up some stuff along the way and made it work again, just the once. I mean, it seemed like it was only good for the one trip, or why the heck would he wait around from the 1860s (or whatever he said) onwards?
2)I vote CCTV footage of Torchwood 1.
3)At first I thought he was sensing the Master waking up again too, but given the above comment that Time Lords haven't been able to sense each other before, maybe it was just overly suggestive cross-cutting on the show's part. Moment of realization, rather than tingly Timelord senses. Barring that, if RTD decides they DO now have tingly senses, maybe it was proximity. Or maybe, before the war, all Time Lords were a sort of constant presence in the telepathic background, so one wouldn't stand out, but since he's alone now, the sudden presence of another is easily felt. (Not sure how sad it is that my brain coughed up all those different explanations in about 30 seconds.)
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2)I vote CCTV footage of Torchwood 1.
3)At first I thought he was sensing the Master waking up again too, but given the above comment that Time Lords haven't been able to sense each other before, maybe it was just overly suggestive cross-cutting on the show's part. Moment of realization, rather than tingly Timelord senses. Barring that, if RTD decides they DO now have tingly senses, maybe it was proximity. Or maybe, before the war, all Time Lords were a sort of constant presence in the telepathic background, so one wouldn't stand out, but since he's alone now, the sudden presence of another is easily felt. (Not sure how sad it is that my brain coughed up all those different explanations in about 30 seconds.)