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Unless you are planning on collecting seeds, cross pollination is not an issue. These articles will help explain more:
https://www.gardeningknowhow.com/edible/vegetables/vgen/cross-pollination.htm
https://www.gardeningknowhow.com/garden-how-to/propagation/seeds/controlling-cross-pollination.htm

It depends on the type of pre-emergent and how long that pre-emergent stays active in the soil. If it is a long lasting pre-emergent, then yes, it will stop the pumpkin from growing. You may want to start some seeds in paper cups and then once they sprout, transfer the cup and all into the treated ground. This will get around the pre-emergent as it will not affect them after they have sprouted.

I would guess pumpkin. A seed from a Halloween pumpkin frequently can make its way into flower beds or vegetable beds and grow as "volunteers" the next year.

Sounds like you may have vine borers. This article will help:
https://www.gardeningknowhow.com/edible/vegetables/squash/squash-pests-identifying-and-preventing-squash-vine-borer.htm

This article will help as it also applies to pumpkins: https://www.gardeningknowhow.com/edible/vegetables/squash/why-squash-leaves-turn-yellow.htm

As long as the terminal bud was not destroyed, they will keep growing. The terminal bud is the end of the vine. That being said, with the plant being so small, they likely did damage the terminal bud, so it is best to plant new seeds ASAP.