Vislor, you have tons of ideas that you are just tossing out one after another. At this point, you should try actually play-testing them. At the very least, you should think very carefully about your favourite ideas, considering how they would actually play out in a game. What is the intention behind your design? What interesting decisions are added to the game? What negative impacts could there be?
If you post ideas with more reasoning and consideration, you'll probably get better discussion and feedback. Right now, it looks like you are asking about the first thing that comes to your mind, and the next thing, and the thing after that, looking for affirmation and trying something else as soon as anybody says something negative about it. Probably nobody here is actually playtesting your ideas, so any negative feedback is speculative. You should feel free to offer counterpoints about why something
could work, and to test things out as well.
Regarding your most recent ideas:
I could just get rid of these plague tokens and try something akin to "Confusion" from Donald X's original game.
INFECTION $0
It has no function or card type (other than INFECTION!). It is just there and will harm your hand by being there. You can obviously trash it or find cards in the set which will help you get rid of them/dish them out to others.
ETA: How about this idea?
Each player has an INFECTION mat. If the mat is empty, when they gain an INFECTION Card it goes onto their mat. If not, it goes into their discard pile. You have to trash the INFECTION card from your mat before you can trash one from anywhere else.
Confusion was scrapped because it just doesn't add anything interesting to the game. Curses are harmful junk. Ruins are slightly less harmful junk which also have a few interesting interactions with cards due to their Action type and the diversity in the pile. Confusion would just sit in the middle without adding anything new.
The idea with the mat still doesn't change it very much, and you don't explain how it's possible to trash a card that is stashed on the mat. Is it a special mat that counts as part of your hand when you play Chapel or other trashers? Do you need some new card that specifically lets you trash from the mat? But again, this slight wrinkle just isn't that interesting. It's still too similar to existing junk cards.
Taking this idea further...what if I made it so you could pay $1 any turn to move an INFECTION card from your hand or discard pile to your INFECTION mat? Then at the end of the game any INFECTION cards left on your mat count as -1VP.
Does this action use up your Buy, or is it an extra thing you can do? I think that this may make the junk even less impactful. It's quite common to underspend (e.g. have $6 but buy a $5 card) so it would not be difficult to come up with the money to quarantine your Infections, especially if you allow pulling them from the discard too. The -1VP doesn't matter much compared to getting the card out of my deck -- I'm happy to trash Estates, after all.
Or another idea for plague tokens if I decide to keep them:
You start with 5 each. You may pay $1 per token to pass as many as you would like to the left at the beginning of your turn. If you have more than 5 plague tokens you may not buy any victory cards that turn.
ETA: ACtually that would probably need to be scaled to the number of players. ie: 2 for 2 players, 3 for 3 players etc...
The scaling issue will still be there if you have cards that distribute tokens. Something like this might be interesting as a separate stand-alone mini-expansion that just adds this extra mechanic with no cards.
Though there may be other problems. First, paying at the
beginning of your turn just doesn't work. Other than durations, you will have no money to spend at that time!
Also note that (assuming Plague tokens are still worth -1VP each) you are offering a 1:1 ratio of cost-to-VP, which is better than the ratio for any of the basic VP. You could let the tokens build up and then pass all of them to the next player for a huge point swing on the turn you end the game. The "can't buy VP cards" clause may force you to deal with them earlier, but there are often ways around it. Various gainers (especially Remodel variants) would get past that restriction.