I assumed during regular cleaning I should be soaking the shower screen and all attached in puly caff while flushing the machine, but the shiny shower screen plate that comes off with the screw has now been tarnished like this. Is this bad, and should I not have done this?

Well, it's useable, if that's your concern, and before the 2018 models, it was brass one, I believe it's called pre-infusion chamber, it has holes to evenly distribute water flow.

Thanks, yeah thats my main concern, so this is supposed to get tarnished like this? Or people generally don't wash this? I would assume this would come in to contact with some coffee oils and eventually need cleaning.

That looks like aluminum, and if so that surface corrosion/spalling seems inevitable and eventually may lead to need for replacement. "Lead-free" brass or SS would probably be more durable, at least IMHO. May have been changed by manufacturer for cost savings.