[Octopus]

Don't worry too much. Any hands you are missing are near 0EV anyway. If your opponents were paying attention, then being that tight would hurt you (they could read you better), but they aren't.

I doubt that it is folding the early limping hands which are depressing your VP$IP that much (though they certainly contribute). A bigger effect is that it will be raised in front of you more often, meaning that you are folding more often in late position. Take a look at the position stats in PT to see if this is right.

Also remember that your pre-flop play should be informed by how aggressive (and loose) your opponents are post-flop.

As for your specific questions: With 2-3 random limpers, I'll play A2s, K8s, Q9s, J9s, 98s, ATo, KTo, QJo, and 22. (With some limpers, I'll play even more hands. With some fewer.) If the blinds were at all tight, I would raise with ATo and KJo, or better. ATs, KJs and TT are worth a raise even if they are sure to call.

Finally, unless you have a lot bigger pre-flop problems than we are talking about here (like you cold-call raises with KTo), then your pre-flop mistakes are not hurting you much. If you actually are a 4BB/100 winner at .5/1, then I seriously doubt you are losing at 1/2. (Keep in mind that 100,000 hands is barely enough to nail these numbers down even to within 1BB/100, and that assumes that you are not getting better over time.)