Just bought a 99 Cobra, tune up tips?

In my opinion

I would do all that you have mentioned above and maybe even consider investing in a chip by diablo(Pred) or SCT and get it dyno tuned

Change the plugs on a stone cold engine! If it's warm, you risk pulling threads out of the head because they are aluminum.

Change the oil and filter.

Change the antifreeze, flush and refill.

Change the fuel filter.

Run some injector cleaner through the system.

Change the PCV valve.

Things such as oxygen sensors, EGR valves etc...change as necessary, for instance...if the SES light was on.

Change the transmission fluid. Regular ATF fluid goes back in there.

Change the diff fluid. I've changed rear end fluid on 8.8 straight axles. I'm not sure how different it is to do with IRS. I don't know if if holds more, or less.

Don't forget to bleed the brakes as well...

I would think about cleaning the MAF. Also, I use antiseize on plug threads. Don't know if will help but don't think it hurts anything. I would consider getting a hand held tuner and datalogging some engine parameters. May help explain "miss" at high RPM's.

I would Seafoam it. Also, be careful on the plugs, I blew one of mine out of the head shortly after a change.