Scenario 1 -
No risk. No STD goes through clothing, and you had your boxers on.
Scenario 2 -
If you had your clothes on, you have no risk of anything genital. If you touched her in the area where she had this red spot, and it was herpes (it doesn't sound like it, but let's assume it was), and you had a cut on your finger, it's possible that you could get herpetic whitlow. This isn't a common condition, and loads of things cause reds spots - shaving, irritation, normal skin fluctuations, clothing, etc.
If you do get whitlow, you won't miss it. It's very painful. This isn't something you'll need to look for.
Scenario 3 -
No risk. Again, STDs can't transmit through clothing.
I don't know what you mean by she "cut the lube with her teeth". Did she open the lube packet with her teeth? If this is the case, then you have no risk for anything.
In order for STDs to transmit, you have to have direct contact with someone's body or penetrative sex - either oral, vaginal, or anal sex. Some STDs transmit through skin-to-skin contact, but it's oral, vaginal or anal to mouth, vaginal or anal. Herpes can be transmitted by rubbing your penis on someone's vagina, for example.
You had none of these things. The only risk you MAY have is for herpetic whitlow, and that's a big maybe. You don't know if her red spot was herpes at all. I wouldn't worry about any of this at all. If you decide to continue these activities, and have cuts on your hands, you might want to consider latex gloves.