Some things that weren't mentioned:
Butch rides away on the motorcycle into the sunset which has a license plate of GRACE.
"I think I cracked a rib." = Adam and Eve (bit of a stretch in my opinion for that one though)
Why did MW let Butch go? He redeemed himself in a way through that, as well as he could have been given the case by then (remember the film is out of order and the last shot is Butch leaving with Fabian).
"Is that what I think it is?" means not that he knows exactly what it is, it simply means that he thinks its something, and he's asking if that's what it is. The fact that Jules automatically knows what he's talking about means that it has to be something awe inspiring that was very unique. He wouldn't say that about gold or whatever unless he was a total idiot. Plus, gold, diamonds, money...that stuff doesn't glow like that, and it certainly doesn't explain how the guy that they shoot glows too, unless you want to say that he has diamonds stuck inside his chest lol.
Only questions though:
Why was Marvin killed if he was helping Jules and Vincent?
What was Lance's role, seeing as how he helped revive Mia, but he definitely has some sort of a metaphorical context (look at how the guy resembles Jesus - long hair, beard, sandals, light robe-like clothing)