Odd, were you unable to get it running with all the stuff intact at all? I've mostly been using HANS when commenting out patches to see the changes they make. I've never had to take any files out to get it to load, with exception of replacing the rom with another game. To get around removing the patches when injecting different games you can also rename the rom to the standard vc_rom.bin. Patches are only applied to the rom of the same filename it seems.Sorry about the double post, but I feel the need to mention this.
If you are more comfortable using HANS to modify the Pokemon VC game files, there's something you can do to get the game to boot with HANS.
Basically, just delete all of the leftover junk patches and JP/EUR language files. It will significantly reduce the size of the app, and in return, makes it work with HANS!
As a side note when I commented out [fight_ret] and [fight_ret_c] the games would get out of sync when battling with an untouched version of VC Red. Namely damage not being the same across both games as one pokemon would faint on one 3DS with the other 3DS showing both as alive. This would end the battle on one 3Ds while the other was stuck waiting for communication.
The patches after that seem to only deal with the graphical changes in moves.