There's a toolchain installer for Windows available which you could use to install the CLI:
After that, it should only be particle update and particle setup. The setup part should be able over the app, or over some community tools through the browser:
I'm not sure about the drivers, but if you follow the steps, it shouldn't be too hard to install. And generally, that should be a one-time thing. The same is true for the CLI, which is useful in many scenarios.
Could you elaborate a bit on that? Flashing an app from the web IDE will automatically update the system firmware if necessary. If you can put it in safe mode, OTA should still work. If safe mode isn't possible, you'll have to use DFU mode.
"force the Wifi credentials", I'm assuming you'd like an input which you can use to set up your credentials, which is not the app? If so, take a look at the above mentioned community project, which appears to do just that. You can also use a serial terminal if you're comfortable with that, provided yu've got the serial drivers installed correctly.
"Force stuff into the Photon", Yeah, no clue on this one. What 'stuff' are you referring to?
Is there anything in particular that you're struggling with? Perhaps we can help out.