I build automated translation tools for a living (see DMS Software Reengineering Toolkit. In my 15 years of experience doing juist this, it isn't worth the trouble to build ("customize DMS" or do something similar with a similar techology if you can find it) a translator for 30 * 1000 lines of code.
You might be hoping for somebody to have done this in advance, "Gee, wouldn't it be keen if somebody built such a translator and I can just use it?" Such a hope is pretty forlorn. The problem is that every source application uses some arbitrary combination of input technologies (you're probably using PHP, MySQL, JavaScript and some weird libraries) and want some arbitrary configuration of output technologies (ASP, TSQL, JavaScript, C# libraries). The space of input/output configurations is too vast for you to have any real chance of encountering at translator that somebody might have built that matches your needs. Therefore you'll need a custom translator. Ooops, back to the previous paragraph.
You can pray for miracle. But I suggest you clean up your PHP files and live with them. The world is full of "beware what you build, because it will last a lot longer than you expect". Choose your technology and architecture more carefully next time, so you don't end up with "messy files".