IMHO there should be no background checks, that is what "shall not be infringed" means.
No constitutional right is absolute. Not every gun law - in the opinion of SCOTUS (and that's what counts) - constitutes an infringement.
As applied to the subject of background checks, given that Heller makes it clear that felons and severely mentally ill persons may be forbidden to own and possess firearms. Given this fact, at least some background checks are, therefore likely constitutional. (This does not mean they are effective, just that under Heller they are likely constitutional.)
However, this does not mean that background checks could not constitute an infringement upon our 2nd Amendment rights. Waiting periods have already been ruled unconstitutional. A background check system that is not effectively instant the vast majority of the time and/or has no time limit is almost certainly unconstitutional.
Of course, if we lose the upcoming election or the RINOs cave and confirm an Obama appointment, then Heller will likely be over turned and we will have to do our best to pass an amendment to restore our 2nd Amendment rights.