Thanks for the feedback! I made some changes to address your questions so the new version (1.3.2) should be helpful.
1) If you missed a hit and immediately have to reload, you will be attacked twice. Once for missing and not immediately taking Them down. And again for reloading and giving Them the chance. If you're having trouble with this, getting a P. Mag might help a lot.
2) You only roll to check if you will face Them when you move into a new Place. The new version has changed the rule to make it more clear.
3) The penalties only happen to your Hit rolls.
4) If you mean "SELL for COIN" under FLESH, this was the old name for currency in a previous version. You collect and use EYES to buy things instead. You can find a small box to keep track of it under the INVENTORY heading.
5) Yes, you can only start tracking and returning to old Places once you get the compass. They will disappear otherwise. The cutouts can be physically printed and cut to keep track of inventory and your map.
For inventory, the items can be placed on your inventory slots. You have a starting limit of 4x4 slots (-1 from your Pistol which cannot be removed) to work with. Note: The Triple King takes up 4 slots!
For mapping, the places can be arranged on a surface or paper to keep track of how things are laid out or connected around you. I realize mapping can be a little obscure. So I will try to make something for that in the next update.
I hope you have a good time playing!