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Academia is rarely easy. As the old saying goes, "The simplest of tasks can be made impossible if enough meetings are held to discuss it." ...and higher education faculty / staff / admin so do love their meetings. They have meetings when to have meetings.
Technically, there shouldn't be much of an issue. I don't use Flash anymore. Hype is my replacement. There are some features Flash could have done better, such as working with vector content or Full Screen views, but Hype is pretty good. HTML5 has emerged as the new standard for interactivity on the Internet and Hype is a great way to get started / more involved in creating HTML5 content.
I think the problem is getting the content straight. If you're assuming the role of a consultant for a higher education project, expect to be paid. They usually have the money and it's not worth the frustration if you don't get paid well. In fact, I feel like they respect you more the more you charge them.
I'm not sure how PHP is involved if it's a front-end project. Again, that's a matter of getting the content straight. Watch out for feature creep. Get paid by the hour or be prepared to charge for extra hours. Something like this can spiral out-of-control.
Try to get as much information upfront. If you don't know something, like PHP, that can certainly make the job a lot harder. That alone might be reason enough to not take the job. Improving your programming skills while working on a project can certainly add to the stress. It can also lead to massive security issues. Bad PHP code can cause big problems.
Being straightforward might help too. If you don't know the PHP part, then maybe they can team you up with someone that does. Creating a good working environment is also critical.
I don't know the scope of this project. But based on what you wrote, maybe it is too much work for one person. Mixing design with development is possible, but it's a lot of work and stress.
Although, projects like this might force you to improve your skills. I've had a lot of tough projects where I had to learn by doing. It's made me a better developer / designer.