Those mods worked fine for me, using what appears to be the identical RTC module, so are you absolutely sure that the SQW/INT output is changing state properly? Check by simply programming the RTC to output a 1 Hz square wave on SQW, rather than fiddling with alarm code.
Check the continuity from the module connector (better, from the Arduino) to the actual IC SQW pin using a multimeter, to make certain that the mods didn't introduce a short circuit or break a PC board trace.
If you have another, unmodified version of the DS3231 board, you can test the code (and alarm output) with the board powered normally.