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91 4 Runner runs rough at idle in gear

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Hi!! I am new to the forum. I have Jeeps so that is where I hang out, but my brother has this 4-Runner and we are working on it for him. Here is the deal:

We have installed new exhaust system, new wires, new sparkplugs, cap and roter are going in tonight. The truck was running rough. It is a 6cyl. It never had much pickup even when it was new. So we did the above stuff, and now it only runs rough with you idle with the truck in gear. If you pop it out of gear, it will bring the idle back to around 1000 and run smoothly. Any ideas on what is going on? We tested the vacume and it seems good.

Thanks for your help!!

Jill Stearnes
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