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Q: what does my car suppose to idle at when it is in gear. on 2006 Subaru Legacy

I had a tune up,with someone i have used before.plugs wires,etc.also transmission was flushed and added new fluid,then had the cv joints changed.when i picked it up it was idleing real low,and the engine sounds like a log truck.and they say there is nothing wrong,but i had to argue with them.that it was running fine when i brought it in.i also am aware that when a battery is unhook,the car has to after a week it sometimes idles low about 500 rpms.when you stop.and still there is a faint miss,even after they said they tuned it up.we paid 900 dollars for all the repairs.and it is running crappy,and they there is nothing wrong, and being mechanically inclined i cant figure out what is wrong,can you help?
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thanks.already done that and there is no problem code.have checked everything possible,and I believe it is in the transmission.when you come to a complete stop,and your in drive.not everytime it will flutter like it is low rpm's but you can shift in neutral and then back in drive and it will stop.when the shop changed the trans fluid,something messed up,or it was about to mess up.will have to take to trans shop.
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