I'm with MortFurd here. It is irrelevant whether snakes and TVs can detect infrared, humans can't. Yes, it is theoretically possible for someone to have some kind of detector implanted in their foot during an opperation for a shrapnel wound using the shrapnel as some kind of transiever and designing it to cause as much pain as possible when a TV remote is aimed at it, but ignoring all other IR radiation. Call me skeptical, but I find this a little unlikely.
Implants aside, I would say this is definately paranormal. IR is easily absorbed and remotes are incredibly low power. The most obvious thing to note is that there is much more IR radiation around than just that from remotes, so we need a good reason why only remotes are noticed. The low power means that a remote would not be capable of causing a macroscopic piece of metal to vibrate, or even warm up. I suppose microscopic pieces associated with the main piece could have a more pronounced reaction due to smaller mass, but molecular scale metal would be absorbed by the body and so anything the remote could have a significant effect on should no longer be present.
As for detecting a remote signal through clothes, this is borderline. It is possible that a signal could get through thin clothing such as a t-shirt, but trousers and socks seems unlikely. I will try a little testing when I get home to see how likely this is. As already mentioned, humans absorb IR extremely efficiently, so unless the shrapnel is right on the surface nothing would reach it anyway, regardless of clothes. Would it be possible to confirm where the shrapnel is, and also what it is made of? I also notice you said that when you first found out about this you were sitting on the remote and had someone else between you and your uncle. There is no way any IR signal could pass through another person, so if this is the case it is definately paranormal.
As a completely unqualified, non-medical opinion, there is nothing vaguely paranormal here. You said that the pain lasts for at least a day and that there is also a constant background. You also implied that he spends a lot of time lying down, watching TV, and presumably using a remote. So, occasionally the pain happens around the same time the remote is used. Since the pain is almost always there and the remote is used regularly, somehow this doesn't seem surprising.
As a final point, you said that no-one is trying to fool anyone. Firstly, you might not be, but with $1 million at stake the JREF can't be too careful, so you shouldn't take it personally if people suggest this and if steps are taken to ensure that you aren't. Secondly, just because you are honest does not mean everyone else is. "Bored Uncle Plays Prank On Gullible Nehpew", in other news, "Dog Bites Man". Paranormal this is not.
