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Some questions about the quests related to the mines in Redding.

I'm currently trying to clear the mine of Wanamingos and find the chip. I've killed several already and smashed a bunch of eggs, but they just keep on coming and my crew can't handle them all. Will they keep spawning until I do something special?

And once I find the chip from the mine. Will the decision of who receives it affect my reputation negatively? None of the options sound good to me.
Redding is a totally optional area, so whatever you do or don't do there won't screw you (although it affects the game world). Give the chip to whomever you like, you won't get punished for it. Enjoy the freedom of Fallout.

The best way to handle the Wanamingos are aimed shots at the eyes, most critical hits ignore armor and if they're crippled they run away in fear. If it's too troublesome to defeat them now you can leave town and return when you're more powerful (level 15 or so) and better equipped or simply skip them. There are easier and more rewarding quests to do in Redding or other locations.
They don't respawn, but there are a lot of them, and depending on where you enter the tunnels you may end up fighting quite a few at once. If you have Fast Shot or aren't particularly skilled with aimed shots, you'll need a very strong weapon to take them out. A Combat Shotgun just won't cut it here unless you're getting crits every shot. Personally I've found that shots to the air intake seem to have a better chance of killing them outright, but eyes are better for disabling them. This is also an area that's really rough for party members, so you may want to adjust their combat AI accordingly.

If it's too hard, just come back later. There's no time limit.
Thanks for the suggestions. I managed it without any problems by having my party stick close together. As for the chip quest, I might just keep the balance and not give the chip to anyone!