"the Rules Committee or Senate Desk never assigns it an HR or S number" is wrong because it is a Billing Clerk who assigns a number to a bill
"a special interest group lobbies a Senator too much" is wrong because one senator isn't enough to kill a bill, but it could be correct if many Senators were lobbied to that end
Which leaves us with:
"a committee simply doesn't address it once it comes to the committee"
This is actually possible. If the committee doesn't address the bill and addresses others, it just won't be voted and eventually will die.
"the bill the Senate passes is too different from the one the House passed and they cannot reconcile it into a comprehensive bill that satisfies both chambers"
This can also happen since if the law is changed so much from what it once was, it might serve no purpose for its creators and they most likely won't want a version of it that they don't agree with.
"the President lets it sit on her/his desk for too long"
If the president does not sign the bill and cannot return the bill to Congress, the bill dies by what is called "pocket veto"