Is it crazy for a PhD student to pay open access fees out of pocket? I was preparing to submit a manuscript to a journal when I made a fatal realization: the journal publishes everything as open access and the author(s)/institution/funding agency must cover the cost ($500). This was a solo side project that I undertook on my own time with no co-authors nor outside funding. I was not expecting to publish this as open access as I was unaware of this policy. In fact, when I initially targeted this journal I thought that some articles were open access and others were not. Upon further inspection this is not the case. I'm clearly at fault for not being diligent enough about the journal's policies.

Now this situation would not be such a big deal except that 


I'm a third year doctoral student and will be on the job market soon (I need pubs ASAP!); 
I was planning on submitting this article and subsequently switching my focus to the dissertation; 
It would take a significant re-work to tailor this paper to another journal as it is somewhat niche: the journal focuses on software publications across a range of disciplines, requires a fairly specific format, and limits articles to 3,000 words or fewer (note: I am not in a traditional STEM field, so I feel that my options for target journals are quite limited).


Am I crazy for wanting to just submit the paper and pay the open access fee out of pocket? $500 does not seem exorbitant compared to other journals' fees. Unrelated to my current situation, a few weeks ago I spoke with my advisor about creative ways to fund open access, but he stated that our university does not have options for funding - this must come through grants. It doesn't seem right asking him to cover the fees as he was not involved in the project and is not a co-author.

In this question, @ff524 suggests seeking funding through PLOS or a fee waiver through the journal/publisher. Other questions on Academia SE result in answers suggesting that authors request funds through the university, library, etc. When is it appropriate to ask for a waiver and/or seek funding from an outside source? Prior to submission, during submission, or after a paper is accepted? It seems like a massive waste of time to seek funding from multiple sources only to have a paper be rejected outright. At the same time, it would seem like withholding relevant information to wait until after a paper is accepted to ask for a fee waiver.
I don't think you're crazy at all. From a purely economic point of view, although $500 sounds like a lot of money, it is quite insignificant (in a US context) compared both to your future earnings once you graduate, and to the present potential earnings you are foregoing by attending graduate school in the first place instead of working at a "real job". Thus, if you truly think that paying the fee will help you get on with your other research projects and graduate faster and/or with a more impressive publication record, then, assuming you can afford to pay the fee without sacrificing other important or crucial things at least, it seems to me that paying the fee is a reasonable decision.

With that said, I think a note of caution is also in order. My main concern is that a good proportion of the journals that charge open access publication fees are predatory journals, and given that you are a graduate student and new to publishing, there is a risk that the journal you are considering publishing in could be one of those. I would therefore suggest not paying any fee until you have made absolutely certain, by consulting your advisor or other experienced researchers, that the journal in question is a reputable one and that publishing in it will actually further your career and goals. Good luck!