It seems you missed the second(2) step in the install instructions in the above post where I mention the need to make sure the azp.exe actually gets copied to the game directory. I think it gets blocked by your system and you need to add it to the exception list. The same goes for the Files.a and Directory.a files, make sure they're in the game fiolder before you run the PatchMe.bat file.
The shop issue is known, but I haven't gotten any confirmation if my fix for it works. This bug only happens to some people, I don't have that problem, so it's very hard for me to see if I fixed it. My latest attempt can be found here, just copy the files to your game directory and make sure the RenderedItems folder is empty to make sure you re-render the old screwed up images.
http://rapidshare.com/files/399965405/BSM_1.01_Fix1.rar
The foregrips in not meant to be taken off, it's due to some engine limitation so you have to live with it. It's also the reason they can't be bought in shops, only ordered though Uribe.
The stock issue must be on your end, it works fine for me. Which version of the WEAPONINFO are you using? Could be that I messed up the alterative one, if that's the one you're using.