Ah brah, that bites. The dowels are quite important. They are relevant to vibration! as well as increasing the amount of torque necessary to break the clutch assembly loose (I guess it would be a shear strength type of thing).
If you go to any clutch or flywheel manufacturer's site and check the FAQ, it should say this. You could print that stuff out (from as many sites as you desire - more sources are better!) and take it to the shop. It seems to me that it should be on them (their nickel) to R/R and make things right since they admitted not using the dowels. Also, ensuring proper torque specs is critical as well (as well as torquing in a star pattern, in stages).
Also, if the shop is unreasonable, let us know if you paid with a credit card - there can be another source of remedy if you did. As always with this type of thing (though it makes us sick), be real nice and calm when you go back or they're likely to tell ya to take a hike.
I really would try not to drive the car too much if you can - those torsional vibrations can really rip apart the driveline and bottom end of the motor.
Good luck with it bud.