Rough Idle after head gasket replacement...

My 2006 TRD 2wd developed a head gasket leak at 170,000 miles which I had repaired at a great local shop here in San Diego. They did both sides, valve job and head gaskets. I noticed that I had a slightly rough idle when cold after driving the truck for a couple of days. The shop agreed and has since checked the fuel system, valve clearance and cam timing. They have found nothing wrong, but I had a smooth idle before the work was done. They finally said that it may be a lose rear motor mount as the shaking goes away when they jacked the transmission up a little. Does any of this sound legit? I like this shop, but am considering getting a second opinion before we start replacing things I consider unrelated to the issue. Thanks for any thoughts on this subject... Scott