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My real question is then, what specifically should I learn in order to make myself more well suited to taking the type of offers that current job listings are looking for?If you're talking about web jobs, I'll point out that you have a rare specialization that you've acquired at great difficulty and expense that puts you head and shoulders above the average developer. Why throw that away before even trying to use it? There are jobs for Comp. E.'s out there in the areas I listed in my original post, though they take effort to find. Don't settle for mediocrity.
If you're determined to do it anyway, a solid understanding of software engineering, distributed systems, database theory, and software security will serve you well. Languages to pick up are Javascript, either Java or C#, and one of the dialects of SQL.
> As far as internships go, I'm completing my masters in one year and would only have time to pursue an internship in possibly winter and summer break of next year at best.
Foregoing internships is unwise; those do well at an internship will often be directly be offered full time employment after graduation, if open headcount is available. Even if not, completing internships and being able to describe the work accomplished is a strong positive indicator to hiring managers.