So here's a couple of thoughts (highlight as before):
1. The gun Leonard had at the attack and the gun that Dodd had were the same gun. This lends you to believe that Dodd is the 2nd guy.

2. I think Leonard is Sammy Jankins and Leonard killed his wife through an insulin overdose, who survived the attack. The tatoo "Remember Sammy Jankins" is Leonard's way of putting the thought of killing his wife into another story that happend before the incident. Remember that the story of Sammy Jankins is that the condition is mental, not physical. This means that he CAN have memories. I think if he mentally chooses to remember something as happening before the incident, then he will and he'll remember it. The tatoo also reminds Leonard that being careless about his memory could lead to bad things.

3. Natalie was not surprised that it was NOT Jimmy in the Jag when Leonard pulled up to the bar also decked out in Jimmy's clothes. She refers to him as "The Memory Man" in the bar. This lends itself to mean that Natalie knew Jimmy was going to be killed, specifically by Leonard. So does this mean that Teddy set this up somehow and used Leonard as a pawn in his plan to get rid of the drug dealer and take the $200k? I think so. After the killing, Teddy is constantly around Leonard, specifically around the car -- and the money.

4. Because Teddy used Leonard to kill Jimmy, Natalie decided to use Leonard to kill Teddy as revenge. She knew about the tatoo's and knew all the details of Teddy and knew they matched up. Now there's a part in here where Leonard is being played, but he's also already chosen this path when he writes down Fact 6 after killing Jimmy. I think Natalie is just pushing Leonard along. She may actually be a pawn from Dodd who has put her into all this to keep Leonard away from him and pointed towards Teddy.

5. I think Leonard remembers the basement the way he remembers Sammy Jankins. Same type of situation. Something he wants to forget, yet can't completely forget. He tries to burn the picture, but he doesn't fully burn in and actually keeps it.

From what I can remember -- I missed watching it again last night -- both guns were a 9mm type. The revolver you're thinking about is the one that Leonard used to kill Jimmy, Natalie's boyfriend. He killed Jimmy, had the argument with Teddy, then emptied the revolver in the truck and drove away in the Jag. These are the shells in the truck that he handles when he comes back to kill Teddy. IIRC, both times Leonard handled the 9mm type silver gun, he loaded it in the handle the same way, suggesting a familiarity with it. Plus, when he found the gun in the hotel room, he wasn't surprised and wondering why it was there. He was just kind of ok with it, again suggesting familiarity with it.

The point you bring up about Dodd just leaving town leads me to believe that he was setting up the plan to get Leonard to believe that Teddy was THE John G. In other words, if he hangs around too much, Leonard will think about him and wonder who he is. He knows that if he just leaves, then Leonard will completely forget about him because of the lack of memory and because Natalie will be pushing Leonard towards Teddy.