Things like this really bug the shit out of me, when both parties are at fault.
Dealer is pointing out many things that have no relation to the complaint. Find a new dealer, now.
Vehicle owner/OP has the tools at their disposal to diagnose the car them selves, an Xcal. Granted they may not know what to look for or what to log, but many of us here certainly do and are more than willing to help save money.
My advice for you is this, don't give the dealership any more money. Pay them what you own them and never return.
Go home and hook up your Xcal.
Scan for any pending codes. The drive home should be enough time for any codes cleared at the dealership to reappear. To help you may want to try and get the car to act up.
If a code appears, post it here.
From there we/I should be able to give you a list of things to datalog that will help point to were the problem lies.
As of now, my guy feeling is an ignition misfire; possibly from water in the plugwells or a damaged ignition coil.
Don't "think outside the box".
There is no box.
Do it correct, or do it twice.