I assume you modified right near where the patch applied? There are a 3 or 4 different sections that look about the same, so it's easy to modify the wrong one if you're not careful.

Also, I'm guessing you probably did, but did you run autoreconf afterwards to update configure, before re-running it?

Failing all of that, you should be able to do

Code:
./configure --with-qt-libdir=/usr/lib/arm-linux-gnueabihf
(or whatever the option is... you can do ./configure --help and get a list)


I'm a bit tied up at the moment, but I can try to take a look at it a bit later.