I did something wrong in the Foundry while I was playing (I think I told off some guy walking around or something) while I was on a quest to give the Clerk a receipt I had in a past life and was told to get out by the guards. Now the Clerk won't talk to me and I can't complete the quest without killing him, which I don't want to do because I don't want to make enemies with the faction. I did some searching around and most answers tell me to reload a game from before (I can't- I accidentally got rid of the one game file from before that point) or to sleep for a few nights to see if they'll forgive me (which I tried, but it doesn't work). One other option is to use a save game editor and set the value for "Alarm 1" to 0, which I did but the Clerk still hates me and won't talk to me. Am I missing anything with the game editor? Is there another in-game way to fix what I assume is a bug?

There are consequences to getting on the wrong side of certain factions, and the Godsmen are one of them. That is not a bug.

If you need an item from the clerk, then you should be able to pick his pocket to obtain it. You will need to use Annah for this if your Nameless One is not a thief.

If you followed the modding guide and installed Qwinn's mods, I think resting for sufficiently long will get you back to even with the Godsmen assuming you haven't turned them hostile. Here's the relevant quote from the Readme file for his fixpack:

"Fixes to the Foundry Alarm system. This fix was requested by Colin McComb, the original Black Isle designer of the Foundry. Angering the Foundry citizens will no longer necessarily cut off all Foundry quests. If you mildly anger them, do what they tell you - leave the Foundry and return to calm them down. If you -really- anger them (hostile), run away and stay away for a couple of days to calm them down. If you angered them -and- murdered a Godsman in cold blood, don't expect forgiveness, ever. "

I don't think this matters, but you may also try leaving the Lower Ward entirely and resting elsewhere.