IR Repeater/Redirector - Electric not Optical


First time poster, and newb, so hopefully my errors in protocol will be minor.

What I'm really trying to build is an IR redirector by splicing into an IR lead, capturing the electric driver signals for that IR, and redirecting them to another IR lead that I've spliced into. Here's the full story, and the questions I have at bottom.

I have several different rooms with TVs, but have put all boxes (satellite, AppleTV, DVD, etc) in a closet. Hooked up to each source is a balun that converts the HDMI signal to Cat6. In each TV room, there is a corresponding balun that converts the signal back to HDMI.

Each balun has an IR pigtail that receives IR remote control signals in each room, carries them over Cat6, then reconverts and powers a pigtail IR transmitter in the media closet. This IR pigtail in the media closet is the part I want to modify.

Right now, I have an HDMI matrix switcher to be able to watch the different sources in different rooms, but no way to control anything but the default source in a given room. (Because the baluns and pigtails are hardwired to their sources and output rooms.) I want to create a IR repeater/redirector using the Arduino Uno for these multiple rooms. (Don't worry about how the Arduino will determine which box to send the IR to--it can poll the matrix switcher with RS232 to match source and output.)

I've seen many discussions on creating an IR repeater optically, but I want to do it electrically. I want to splice into the last line of the IR (the pigtail leading from the closet balun to the source), then redirect it to the proper source with an identical electrical signal. I think the best way to do this is to deconstruct the pigtail and redirect the signal through the Arduino. The pigtail is a simple 2-conductor 3mm mono headphone jack, so it seems like soldering wires to redirect through the Arduino would be relatively simple. Since I'm stealing the driver signal for the final output IR LED, I think all I need to do is measure and count the pulses/spaces with an appropriately high sampling rate, and then reconstruct that signal on the right pigtail. (Also, I'm not worried about overloading the Arduino with several people sending remote control signals at once. That's something I can worry about in v2.0.)

With that long buildup, my questions are:

1) Conceptually, are there any problems with that approach, versus a true IR repeater?

2) I've used a multimeter to determine the voltage drop and driver current through the pigtail that I'll be deconstructing. If I've done it right, the driver current is very small, around 250-350 microamps. (I don't mind blowing one up to test the actual current, but haven't done it yet. But the voltage drop between the tip and sleeve of the jack is only 0.35V. How do I account for that, since the Arduino voltages are 10-15X that? Have I measured correctly (i.e., does that number make sense)? Is there a way to reduce/divide the output voltage provided by the Arduino? Will it work by just using the I/O pins on the Arduino?

Any guidance or help, even if only for part of my question, would be very much appreciated.