How to modulate my IR sensor?
There is little information on the Amazon page about these devices.  Only that the output is digital (only on and off) and that the sensitivity is controlled manually by an on board pot.  It would appear impractical to enhance this type of device with out detailed specifications and / or a schematic.

If you would prefer using software to solve some of the problems you listed, I would suggest you use an IR parallax (not the company, the technique) distance sensor with an analog output.  That way the Arduino Uno's analog input can be used to read the sensor and software (sketch) can process (filter) the data before it is put to use.

Added later...

Here is an article describing how to use an IR parallax distance sensor.  Here is an Arduino library design to work specifically with the Sharp IR parallax distance sensor.