Re lining it up, I found if you did it at dusk you could see the laser dot in the distance, especially with a telescope. Then just move it around till it hits the target. But I'd be interested to hear how it was done at 6.5 miles.
Re serial data, this ought to be no different to radio links, where you have white noise then you send some 01010101 bits (ascii U) to get it ready then a wakeup preamble and then some bytes. If it is an AC coupled waveform, the UUUU will bias it to the centre point. Maybe use a 1uF bipolar or greencap, and bias the picaxe side to 2.5V weakly with a couple of 10k resistors in series. If the amplitude is right eg a 4V to 5V peak to peak AC signal, and it is biased as above, it ought to go straight into a picaxe with no further processing needed.