The way I installed ioRtCW is as follows:

Install the game and copy the Main and pb folders (I'm not actually sure if the pb folder is needed, but it can't do any harm for it to be there even if it isn't used).

Create a new folder for ioRtCW and extract the ioRtCW files to it. Put the Main and pc folders in this same folder. You can uninstall the game now as it isn't needed. The ioRtCW folder has the ioRtCW engine and the RtCW data files that it needs, it doesn't need the original game executables.

Launch the game with the ioWolfSP executable.

I'm pretty sure that you shouldn't be mixing up the various unofficial patches, as ioRtCW is an updated game engine, whilst Knightmare's 1.42d patch is a patch for the original engine. They are like different branches as both are unofficial, so do their own things.

Oh, and if you want widecreen, follow these additional steps.

Launch the game, set up your controls and such, then quit. The config file should then have been created. It should be saved in your Windows user documents folder, for example: C:\Users\<Username>\Documents\RTCW\main

Edit the wolfconfig.cfg file in a text editor (Notepad, Notepad++, or whatever your preferred choice is).

Find the line containing seta r_mode and change the value to -1.
The change the lines seta r_customwidth and seta r_customheight to your desired screen resolution (e.g. 1920 and 1080).

Hope this helps.