Skippy620;
I'm not sure what you mean buy the "Performance Stage #2 package " but I assume its the pipes, AC, PCIII, Cams, pushrods, etc. I would not get the AC kit from Freedom as they only provide the SE kit with the POS paper filter element. See the "roll your own" thread for the parts you need for the stage 1 AC kit. The install should take about 4 hours for the cams and an hour or so for the exhaust. I would say 4-6 hours for the whole job.
As far as the Dyno run, yes I would do it. The map from Freedom should get you close but a good tuner can do much better, specifically if they tune each cylinder independently. Each motor is a bit different as well.
Best of luck with the setup, I'm sure you'll be happy with it.