Tom is 100% right...those spots that that you've been so worried about are definitely femoral pores, and are perfectly normal! All beardies actually have them, altlhough they are much more prominent on males, so I would say that you definitely have a male, since his are pretty large. On most females, they are so small that you can barely see them , although there are exceptions to every rule.
As far as the end of his tail is concerned, it looks like it was either bitten off by another beardie in a fight, or he had to have it amputated for some reason. My oldest male, Ming, recently had to have a portion of his tail amputated due to an infection, and the end of his tail looks very similar to what you're seeing on your beardie. If either of these things happened fairly recently, then the black spot may be a bit of scab which still hasn't come off. You might try giving him some long soaks in warm water to keep the skin at the end of his tail more
hydrated. Also, applying some pure Aloe Vera gel (you can usually find it in a pharmacy, but make sure it is 100% pure Aloe Vera, and has no added chemicals) to the end of his tail on a daily basis for a while may help it to heal up a bit better. If there is no raw flesh on the end of his tail, you could also use olive oil as a moisturizer on the end of his tail.
You also mentioned that his jaw is a bit lopsided. If so, then it certainly isn't very apparent in the pictures that you've posted. However, if you can definitely see a difference in the shape of the jawlines on either side of his face, then I would recommend your having him examined by a vet, and have his calcium levels checked. If he didn't have proper UVB lighting prior to your getting him, the difference in the two sides of his jaw may be due to Metabolic Bone Disease. In some cases Metabolic Bone Disease can be reversible, to a large extent, once he starts receiving a good liquid calcium supplement, and you provide him with a good fluorescent fixture, along with a fluorescent tube bulb that will provide him with adequate amounts of UVB. The ZooMed Repti-Sun 10.0 Desert bulb is an excellent bulb which would provide him with adequate amounts of UVB, as is the ExoTerra Repti-Glo 8.0 fluorescent tube bulb. ExoTerra also makes a Repti-Glo 10.0 bulb, but I would stay away from that, as it has been known to cause eye problems in some beardies, due to the fact that they sometimes actually throw too much UVB. Either of these bulbs would be an excellent choice, and they should be changed every 6 months, whether the bulb is still working or not, as, after that period of time has passed, the bulb will no longer throw enough UVB to keep your beardie healthy.
All in all, from the photos that you posted, although your little guy may have some health problems, he really doesn't look all that bad, and with good care and lots of love, he will get better and better as time passes. Good luck with him, and if we can answer any more of your questions, all of us would be glad to help you, if we can.