Newbie needs help!!!

I hate that my first post is about a problem with my beetle, but unfortunately it is...

My '02 2.0 Beetle is having issues. I drive 114 miles round trip everyday for work. About 20-30 miles into my drive, my beetle will sputter and the check engine light will start to flash. It will continue to sputter and struggle, but if I pull over and let it sit for 20-30 secs at the most, it'll restart fine and finish the trip like nothing happened. I'll have to drive it for a couple miles sometimes to get a safe spot to pull over, and it's like the car is just struggling to get power (going to around 4k rpm and barely doing 60mph). Doesn't do it in the afternoon or any other time (i.e. when I take it to my mechanic to look at it).

My mechanic is at a loss right now as to what is happening - we've tried a spray bottle with water to get it to bog down again (I've replaced the coil 3 times in it), and that does nothing. The one time I could get it to the shop with the check engine light on, all the computer would tell is random misfire, all cylinders.

I love my car and would like to keep it, but I'm not a fan of getting ran over on the interstate at 5am either. Any suggestion/advise is greatly appreciated!

Thanks to everyone in advance for any help they can be!