l have a 1999 BMW M3 E-36.The AC/Heater only blows about half the time.When l start the car it will either work or it wont until the car is turned off.There are no issues with the electronic panel at all.This was replaced recently.How much will this cost to fix and can l do it myself?

Sounds like a bad final stage unit, commonly called the hedgehog due to the way it looks. It will cause the fan to speed up & slow down randomly, even though u (or the computer if u have auto climate control) have not changed anything. This is a common failure in many BMWs. l have not experienced it, although my auto climate controller went bad once & l replaced it for cheap. It did not know what the interior temp was due to the tiny suction fan that samples the air seizing up.
The hedgehog is located behind & to the left of the glovebox (LHD). It is just a big resistor pack to give u numerous fan speeds. You should be able to replace it for less than $100.

http://forums.bimmerforums.com/forum/showthread.php?p=3349096