purecsqc depends upon a 'small' change that allows setmodel(world, "maps/foo.bsp") to affect more than just qc fields. it will not work with older exe builds. This was aluded to in the readme: 'Expect to need to update'.
Anything before revision 4758 simply WILL NOT WORK.
Revision 4758 involved a rewrite of most of fte's loading code and will likely have introduced bugs in unrelated content, the sort of bug expected from this is primarily just missing textures (resulting in the checkerboard fallback texture turninig up).
my q3bsp testmap works fine with purecsqc. I cannot fix it without being able to reproduce it. No part of fte will clear the screen to green (typically that would be a result of non-conformant sli workarounds, and gl_clear 1 will clear it to red instead).
if purecsqc starts erroring out when trying to load a map after you disconnect, use the start-new-game menu to reset the game state (this is equivelent to setting the purecsqc_state cvar to empty and then disconnecting again). this can be needed if the map does not contain a spawn spot or if the qc errors out some other way that prevents the map from being restarted.
purecsqc expects to not have any ssqc running at the time, because that can affect things in awkward ways (ie: the server changing the world model, adding static entities, etc. that way lies duplicates and erroneous effects). This is specified in the readme.
Use the csmap command to switch maps. It will load up a map automatically. Again, consult the readme if this fails to happen.
your manifest file does not specify the id1 gamedir. it does not even specify the purecsqc gamedir. you should not even need an fmf file at all - especially not a badly made one. fmf files are for stand-alone mods that want to completely break from any existing game, or mods that need autoupdates for some reason (ie: mods where only the fmf is linked and the rest of the data just gets downloaded automatically), and purecsqc is neither of these two types of mod. just install the mod as a subdir in your quake directory, and run the engine from there. load the mod with the gamedir console command, or the -game commandline argument. again, purecsqc is NOT a standalone mod, and fully depends upon quake's content.
the fact that you are badly trying to hack around things by using greater complexity will have resulted in none of the quake content being findable, which is why when you try using the _SERVER_ (which you should not be trying to do, I should point out once again), it fails to find the progs.dat file and gives you lots of errors about entities and noclipping movement.
if you have multiple base games installed in your base directory, you can explicitly choose between them with -quake as well. add -nohome if you don't want to use a home directory.
if you use -quake or one of the other arguments and the specified game does not exist in the working directory nor where the exe is located, it will look at the registry for where you have previously told it that the specified game is installed. if you've not previously told it then it'll prompt and remember the location that you told it.
if you have erroneously told it that your Enemy Territory basedir should be used as your quake base dir, you can override the registry setting with the '-basedir c:/games/quake' argument, and it'll use that directory regardless of where the exe is installed or where the registry says the game it thinks it should be running is.
If you wish to see which base directory etc its using, the location of the home directory, the ordering of the basedirs, the priorities of the paks, and the flags that might be active on the various packages, you can use the path command. This is true for *ANY* quake engine, including vanilla quake, including quake2, including quake3.
randomly renaming the exe will cause it to think that it should always be running a specific game, if that game's 'codename' appears as part of the file name. you can use -quake to override this and revert it to running quake content only. it will already no longer ever try running ET based on the filename, so again, use an updated version of the engine as specified in the readme.