I somewhat disagree with some of the earlier answers on the "jobs applications impact". First, I think it makes absolutely no difference whether you have "submitted to Annals" or "preprint" on your CV. Everyone knows the acceptance chances and will ignore this line. Second, it is really important that all your papers are available on the arXiv or your personal web page. Often, the hiring committee can't judge the applicant's work, and will ask a local expert at the department to take a look at the papers and give an impartial opinion. If the papers are not available, the committee is forced to trust the applicant on their existence, a bad situation all around. Finally, except for the really top journals, having a paper published vs. having it still in a preprint form is of minor difference - if the local experts and/or reference letters are all saying that these recent papers are really good, that's sufficient. From that point of view, you should basically ignore the job application considerations, and always do what's best for the paper.
P.S. If I may make a suggestion, I think it's much more important to choose the right people to write reference letters than worrying about minor points in your CV. Especially now, in the mathjobs era of mass applications, it is the letters that really help people stand out from the crowd. So my advice would be to start thinking well in advance who can you ask for the letters, and learn how to better communicate your results (to them and everyone else).
It is in principle possible that reviews are revised/replaced (as I assume you know).
However, as far as I know, this is mainly done to replace factual errors. From your description it seems to me that your situation might be at the borderline of factual errors and different interpretation.
You could also check http://www.ams.org/mresubs/guide-reviewers.html (in particular the point 'evaluative reviews' to see whether the review is in line with what is written there).
Yet, since you say that the review is not negative, this seems less relevant to your situation.
Now, in case you decide to do anything, in your situation it seems definitely advisible to contact the reviewer directly. As it was not negative it might be a misunderstanding/an honest mistake, and the reviewer might be willing or in some sense even happy to correct the review if made aware of the problem.
I am a fairly frequent reviewer for MathSciNet. My greatest worry doing this is to write something wrong in a review, and by doing so, somehow make a fool out of myself. So, in case an author of a paper I reviewed should ever contact me in a friendly way and point out why my review is not to the point and I then understand that s/he is right, I certainly would try to get this corrected, and be grateful for being made aware of it.
By contrast, I know indirectly (a collegue of a collegue...you get the idea) that if the reviewer does not want to change the review it can be very difficult to get it changed (except there is a direct factual error).
So, you need the reviewers consent anyway, and as André Henriques says, there is no way to hide that you were 'behind' the activity; or even if there was a way to do this anonymously, it should be the default assumption that the author of the paper is the one 'complaining'. This seems another reason for directly contacting the reviewer, as it seems rather more likely to get her/his consent by this course of action, then by one going an official way.
How to phrase the communication with the reviewer: a way could be to not directly or mainly critizise the review, but to just sent the reviewer your point of view. In other words, write somehow your own review and share it with the reviewer. Perhaps only pointing out key differences in passing.
In any case, if you do not care deeply I would at most contact the author of the review; perhaps this works out well, but if not rather drop the matter as further activity might be in vain, and not be worth the effort and negative side-effects.
Best Answer
I really don't think this is a problem.
If there's a good / logical reason to combine the papers (and such a thing is possible by timing), that's fine. But there might be many reasons why it's not appropriate - in addition to what you mentioned above, there might be two different sets of coauthors on the different papers, which can also make it tricky...
However, if paper #2 has already been submitted/accepted/published/is not easily combine-able, then I think you should resubmit #1 at your convenience, to whatever journal is most appropriate. I wouldn't worry about paper #2 really at all in this decision.
In many subfields of mathematics, dissemination of results now happens largely on the arXiv. Thus I think where / when the articles get published is becoming less and less important (although the prestige of an article in a good or top journal can still be useful for career reasons).
I've certainly been in situations like this and it hasn't seemed to be a problem. I've also been a referee of papers in this position (both #1 and #2). In the reports for papers #2, I usually note something like: "this paper builds on the work of paper #1 which appeared 3 years ago on the arXiv...."