No difference in terms of performance. The Mopar intake is just for looks. Compare it's design with a LMI one (the only CAI that actually shows gains at the track) and you will see why. As for your times, C&D has posted 12.4 in their testing on a stock 245 summer tire car. So the 1/4 isn't hard to believe at all. Your 0-60 is better, but switching to a 305 Indy probably accounts for that. You probably just have right touch launching, which is why you do well. Go put it on the track and see what you can do on a prepped surface.
Also who said the timers were inaccurate? I've not seen any one who has used them at the track come up with more than a tenth or two difference (usually the timer being slower than actual). I know I used mine on 4 passes last time at the track and it was on the money or a tenth higher than actual.