I am in the same place you are. I have never compiled a kernel before, but I did manage to get all of the sources together, insert the lirc_rpi.c file you linked too, that I found a couple of days ago myself, and compile everything up. So I am a little further along than you are. Currently I am at the point where I tried to install the module as a replacement to the existing module but I am getting an error saying "Unknown symbol in module". From the little bit of research I have done it looks like there may be a dependency I am missing, or something declared incorrectly in the file. Almost everything I find is in German talking about that code, and I don't speak or read German. If I get it figured out I'll let you know.
I do have a question for you though. Are you trying to control two devices that use the same remote config? Is that why you are trying to put two different transmitters on the pi? I am trying to do something a little different. I am trying to hook up two TSOP because one of my devices runs at 56khz and the other runs at 38khz so I have a clock issue with using a single receiver. I am also working to get the pi functioning as a repeater/extender in addition to being able to control all of my IR devices.
I found some examples where people are running multiple instances of the lircd but that just does not sound right and clean to me. That work around can be found over in the thread
http://www.raspberrypi.org/phpBB3/viewt ... &start=125 which links to their code
https://github.com/phillipsnick/rpi-linux
As far as compiling I used the tutorial over at raspbmc.com to cross compile on a Ubuntu machine. That can be found at
http://www.raspbmc.com/wiki/technical/kernel/ It was not 100% clear to me since I have never compiled a kernel before but I eventually muddled my way through it. The thing I learned in the process is follow the directions to get your "Raspbmc builders root filesystem" setup first. The last step is to chroot to the new file system. From there you can use wget to download the build_kernel.sh script (which by the way their link on the page is broken, there are newer version build_kernel-3.6.sh or build_kernel-3.8.sh). The script will download all of the stuff you need and compile. You will just need to modify the script before you run it to pause somewhere before it starts the make process so you can copy in your updated lirc_rpi.c files into the source.
Maybe you will have better luck than I will. Or maybe someone will chime in with an answer. Either way I will let you know if I figure it out myself.