Shouldn't this combo be quicker?
 

I ran my car last night after I had it tuned and it ran a 12.66@114.75. This is what is done to it: CNC Ported 241 heads, TR 224/228 cam on a 112, FAST 85/85 intake, lid, Hooker super comp headers, TSP true duals, 3.90 gears in the rear. It's still got a stock 10 bolt so obviously I can't launch it has hard as I would like, but that ET above had a 1.98 60' so it wasn't THAT terrible. The thing that I'm upset about is prior to the heads/cam and exhaust, it ran a 12.70@112.33. That's a stock engine with the FAST intake, lid, loudmouth catback, 4.10 gears and NOTHING else. Going by that, the heads and cam and LT's gave me a whole 20 HP??? WTF!!! I hear people gaining 50-70 HP doing a swap like this. What's the deal? The engine is sound and has good compression, so why is it so damn slow? I'm embarrassed at the amount of work I have done to this car to run mid to high 12's with it.

My guess is that your 12.70 was run in cool dry air and your 12.66 was in warm summer weather. Every 10 degree F drop in temperature makes a 1% increase in power. If you were running in 90 degree weather on your 12.66 run and 50 degree weather on your 12.70 run, that's a 4% power difference just because the change in weather. On a 450 horse motor, that's 18 horsepower right there. A changing barometer will skew your numbers even more. Before you blame your new combo, be sure to check the density altitude of your 12.70 run to the DA of your 12.66 run.

Well, I understand the role weather plays in power - the 12.70 run was in 80 degree weather and the 12.66 was in 60 degree weather, but with a lot of humidity. Disregarding that, I figured I should be running closer to 12.1-12.2@116-118 with the mods I have done.

Your 60ft. is killing your et. If you can get the 60ft time lower you should be able to get the et around where you want it. I figured your mph would have been around 116 as well with the mods you have.

Figured out that the tune didn't take in the PCM. Damn '98s. Waiting to get a new PCM with the correct program in it. Should hopefully pick up a bit.