are there advantages over doing it in php over perl?
There is one big one that's probably more relevant from your boss's perspective than from yours. When you leave the project or the company†, it'll be a lot easier (and probably cheaper) to find a competent PHP developer who can take it over.
Will I have a difficult time since I've done almost no php?
It depends on you, of course. I do think that Perl programmers have a tendency to think of PHP as dysfunctional Perl and that tendency makes their learning curve slightly steeper. There are annoying syntax similarities‡ that sometimes disguise the fact that the languages are not at all alike below the surface. Still, it's an easy language to learn and you shouldn't have that much difficulty given that you already have substantial programming experience. If you do go that route, just try to keep in mind that PHP is not Perl. (Deja vu... I've said some of this before at Re: Perl is more intuitive.)
The one thing that makes me pause is your description of this project as "major". I think Perl definitely has some (or, at least, can have some) advantages for a larger project, especially if you have more than a very small handful of people working on it.
† More specifically, when you finally perish in a brief and tragic meeting with a runaway bus which is, as all management knows, the inevitable fate of anyone who becomes too familiar with the evil technical details of any project.
‡ Similarities that probably exist because PHP was originally a Perl program.
"My two cents aren't worth a dime.";
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