Dave: This is a writing problem, not a mechanical problem. The widely separated whether...or is correct, but it's not good writing. An easy solution is to reverse the two phrases represented by whether and or, i.e., put the short one first.
Also, remove the comma before or. Correlative pairs (e.g., either...or, both...and) are not separated by commas.
Notice: The correlative pair is whether...or. Whether establishes a choice between options, as in whether this...or that. Thus, no if is needed; in fact, it's redundant. Save if for establishing the conditions for an action, and you will increase both clarity and professional credibility.
Of course, the real problem with the sentence is the choice of subjects. There is always a crummy subject. It serves only as a placeholder and has no meaning itself. If you really wish to improve this sentence (notice if to establish a condition for the action to follow), then find the real subject, i.e., the rhetorical subject.
More about the rhetorical subject: http://preciseedit.wordpress.com/2010/03/12/the-real-subject-of-your-sentence/
Could we be the rhetorical subject, as in "We aren't sure whether...or..."?