What you need before you start running is get a save with 83 QRs (with unique ids) viewed and all 22 audio logs listened to. This doesn't need to be in a single playthrough, but you do need to do it all without cheats being enabled. Doing this would unlock the "QR Reader" and "Good Listener" achievements respectively, but having the achievements doesn't mean you have the flags set, so I think it's misleading to say the run requires the achievements.

~~If you don't want to go through the work to get the flags then what you can do is replace your save file with one that has the correct flags (I'll link it below). This will also give you all achievements that the save has but you don't, in this case all of them. Your save is stored in "[main steam directory]\userdata[your steam id]\257510\remote", so on windows this is usually "C:\Program Files (x86)\Steam\userdata[your steam id]\257510\remote". Make sure to replace both files, and then next time you launch the game you'll get all achievements and you'll be ready to run the game. A few more important things to note, this will get rid of any playthroughs you currently have, so you might want to backup your files first, doing this will mess with all of your settings, so you should definitely go through them all again, and I'm not sure if this works with steam cloud on, so you may want to turn it off.

The save file: https://drive.google.com/open?id=0ByYTh9vvPxG7QWJWNDR1Y3p0SlE~~

Oh I missed the bit about All Sigils, for that you only need the QR flag, but you can instead hit a death trigger. The most common place to do this seems to be in Escalating Problem (like this: ), but behind spawn in A4 is another good place. Doing this is slower than reading a QR if you have the flag, but only by a few seconds, so it might be a worthwhile compromise.

Hmm, maybe it doesn't like saves from other players, in that case you'll either need to get the flags manually, or do the work-around I posted above, but that can only replace one.