I think they look a lot alike, but I think the eyebrows are off. Eyes are much different. If the hair line and amount of hair on the JD is accurate he has more hair than the missing man- who looks a lot more bald ontop. The circumstances of the case also make me lean towards a rule out.
The missing person was last seen at his mothers in 2006. Even though he was homeless, he was still in contact with his mother. The John Doe was found in 2009 and died as a result of accidently lighting himself on fire. It's possible, but hard to imagine why he would not have made contact with his mother for three years if his death hadn't occured somewhere about the time he was last seen in 2006.
I assume the address listed: 2335 N. 13th St Philadelphia was a vacant building? I didn't look that far because the 3 years was just too great for me between time missing and time found.