Long tubes FTW on the coyote, they are definitely worth the upgrade. They are a PITA to install though, especially on the 18+ because of the AC lines. Long tubes and gears are the next mod's on my list for my Bullitt. I already have the "power pack" on the car from the factory with the PP1 suspension and magneride. As said above, if you like cornering a little then definitely find a car with the PP1, and if you can, the magneride. A steeda front brace does wonders to tighten the front end up and reduce tramlining with the wider tires. The torsen rear is just fun to play with in the corners, night and day between that unit and a trac-lok. The PP2 cars are fun as well, but hard to find, and they tramline like a mofo with the wider fronts.
I know on my car, with the power pack, long tubes, resonator delete, and a lund or steeda tune to take full advantage of the long tubes, guys have been touching 500+rwhp with the Gen3's. With an E85 tune they are over 500. If you want to go really fast, look at an A10 auto with a Gen3. I personally like to shift gears though. The gains on the Gen3 with just a resonator delete are real also, surprisingly real considering how easy a mod it is to do.
I've been looking at either the 4.11 gears or HOPING someone comes out with a 4.30 set to help with the long legs of the MT-82/D4. I'd like to use a little more of the coyotes high reving nature without breaking speeds limits in 2nd gear.....
Both the Gen2 and Gen3 are great engines, I'm just speaking from my Gen3 experience.