As is been stated, any SHO should be running 15s if it's been maintained properly with a good-average driver, unless you live at higher altitudes.
My 1st ever pass at the strip was 16.5, and once I learned how to properly launch the car (it was an MTX) I took that all the way down to 15.2. My wife's first time at the strip (in a near-stock ATX) was 15.17 so yeah, the cars are certainly capable, but maintenance and skill play a big role.
That being said here's my timeslip analysis for you
2.48 60 ft = slow out of the hole. With an ATX you should be able to get pretty consistent 2.2's without much trouble providing you have decent tires and a healthy car. Sounds like you launched like you should, brake-torquing the car, but you either got a fair amount of tire spin or the car just slipped & bogged out of the hole. Or maybe you didn't get your right foot down quick enough. Another thing to consider is your suspension... this part of the run will really be affected by an older, softer suspension. It allows for more weight transfer to the back wheels, causing your car to sqaut in back. When that happens, not only do you take weight off the front wheels (which will let them spin more instead of grip) but you're also taking energy that could be used to propel the car forward and instead pushing the rear end into the ground. How squishy is your suspension? In any case, take that 2.48 down to 2.22 and you'd be seeing a mid 15 pass.
10.41 @ 70 at the 1/8 = Slow E/T but a decent trap speed. This can also be reflected a bit by the 60ft time, but a healthy ATX should be in the high 9's to low 10's with a trap around 70. You mentioned possible transmission problems, if it's slipping or not shifting at the correct RPM's that could account for the slower time. Did you shift the car yourself, or did you let it shift? It's been my experience that, on a stock or lightly modded ATX, it's best to let the computer do the work for you.
16.01 @ 87 in the 1/4 = Slow numbers on both sides. Seeing an 87 trap speed after 70 in the 1/8 tells me the car just isn't getting it done up top. It's not what I would call really bad, but a trap right around 90mph is typical for a healthy car. Once again, consider your transmission as I believe you get the 2-3 shift after the 1/8 mark.
Overall, I don't think your car is down too much on power. Perhaps a little bit, and your exhaust leak could be part of that. A 60k with fresh plugs & wires and a complete exhaust system may give you an extra MPH or two on your trap speeds, but I believe that your troubles like more with suspension and transmission problems, and just old-fashioned practice with launching.