I think it would be pretty easy to loop around the WebAssist File Upload code and use that.
If it were me I'd probably use the base webassist code since it has some nice features, but doing uploads by hand in php isn't too difficult as long as you aren't doing image resizing or creating folders or increment file names which are built into the WA code but can get tricky to do by hand.
This is definitely something we could help you with in a premier support ticket.