How to fix holes in these wood floors?

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Hi! Love the ideas and resources here and I'm really hoping for some advice.
My husband and I have rented a old farmhouse. It's well over 100yrs. old and feeling it's age. The landlord has had very bad luck with tenants and unfortunately this once beautiful home is now very torn up. My parents were friends with the landlord's parents and I was at this house often when I was a child. It's a shame what it is now.
Anyway we were given the opportunity to rent this place for extremely, extremely low rent. We are losing our house to foreclosure and jumped at the chance to have this since our 3 kids won't have to change schools and we won't have to get rid of our pets. I HATE that we are losing our own home but unfortunately due to lay offs we had no health insurance and my husband suddenly had a tumor come up that was testicular cancer. We lost everything due to it. I am trying to make the best of things and make the best "new" home possible for our children but it's very hard with our limited finances. We barely have money for the paint we need.
So back to the floors. We have skids and skid tops, very good, non chemically treated pine that we can cover the floors with. We had planned to do that and I was either going to stain or paint them...whichever was the least expensive way to go. Now I'm wondering if we just can't patch these holes in the living room and paint the existing floor.

For the hole in the hallway we had planned to patch that all along as it's just one hole and there is already evidence of a hole that has been filled with something in the past. I just don't have any clue what to use to patch the holes! I've done lots of research but I'm still confused about what product to use that will be strong enough. I do not want to have to cut a larger hole unless we have no other choice. We already had to do that in the dining room and jack up/replace the beams and now will have to cover that whole floor with the pine wood we have. Due to time constraints I'm really hoping to just be able to patch and paint these floors.
What do you suggest I use for the easiest, most economical way to fix these?
Thanks! Sorry this got so long. Guess I felt the need to explain.
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one of the living room holes..
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