I have just been through the process of fitting the Pink Cowl to my RV 3 and I had the same differences that I think you are describing, essentially with mine one side of the cowl appeared to be moulded higher than the other and the whole top cowl seemed to have twist in it that sitting the front in place saw the rear way off and vice versa. There is also a forward/aft difference in the prop blade to cowl spacing at the inlets as well, I surmised that it is supposed to be that way?
Long story short to make it fit I leveled the fuselage fist then with a laser drew a level line through the centre of the prop hub and down the sides of the fuselage beyond where the cheek extensions would end. This line is where the cowls meet and the tapered cheek extension ends. I then concentrated on getting the inlets level and symmetrical, the now out of whack left rear of the cowl fitted the firewall curve well enough but was sitting nearly 1/2 inch high at the cheek extension, I slit it with the dremel 7-8 inches up the cheek line to make it fit, then trimmed just enough of the top and bottom cowls to meet the laser line. Lots of other minor filling and sanding required at the front as well. It's not perfect but I have the first time builder excuse to fall back on, (the next one will be better!). It ended up fitting OK despite looking like it never would at first. Good luck with yours.