hello LatvianMan,
the project is a bit overloaded with RC5 functions and therefor difficult to get up and running without knowing exactly what the different commands (RC5) are meant for. i confess: it is always a quest to set this thing up. without reading and understanding the (poorly documented) code it will take you some time but maybe i can help.

i will try to explain the basic concept and give you some hints, but if you use a different remote control with possibly some buttons not available, i suggest a different approach: dive into the code and create an eeprom file with the setup values manually. there are only a few, but hacking them into with the remote control is kinda difficult.

there are setup values stored in eeprom every time you hit the power button. these determine the brightness level of the R,G,B LEDs and (because there is no .eep file included) are initially set to full brightness, which results in white color(?). furthermore, the FFT "channels" that are used for the lichtorgel part are also stored in eeprom. these require some patience to get set up.

first try to get the static color mode running. this mode is activated with the "stop" button on my remote control (use the code table http://codefactory.dead-men.de/projects/AmbiLight/ to figure out, if the buttons on your remote control have equal codes). the brightness is set up with arrow-up and -down keys (code 20,21).

the cycle color mode is activated by the "play" button (code 53). it uses the same brightness value as the static mode. speed is controlled by some other arrow-left and -right buttons (code 50,52 - actually there are a lot of different arrow buttons on this remote control!) and ranges from veeeery fast cycling (means flickering) to very slow (1h per full cycle which means it can be mistaken as "static" too). if brightness is set too high, this mode will also result in white light).

now for the most difficult part, the lichtorgel:
on my remote control, there are RED GREEN YELLOW and BLUE color buttons (see the table mentioned above for the codes of these). these are important to set up the lichtorgel function. switch to lichtorgel mode with the "record" button (code 55). choose a color (R,G,B) with the color buttons and use the arrow-left and -right buttons (code 50,52) to change the brightness level. YELLOW sets the overall brightness.

to make it somehow more complex, the FFT channel (treble/middle/bass setting) of each color can (and, for the first setup, must be) chosen manually: use the RED button, then enter a number between 0-29 on the number table of your remote control. the lichtorgel should answer the first digit with 1 white flash and the second digit with a double flash which means it accepted the value.
the same procedure goes for the GREEN and BLUE channel.

as you can see, setting up this beast is kind of a mess. i was so happy to finish this project that i published it without thinking about poor people like you who would try to rebuild it. understanding or even better adapting the code would be much better than just using the HEXfile. i know about the insufficency of the implemented operation, especially the setup. sorry for that!

kind regards, die katze