You'll definitely benefit more from getting the tune after your mods. If money is not an issue to get it retuned later, then go ahead and do it now. I'd personally save the $300 or so and do it after my bolt-ons are on though.

I think it depends on how long its going to be till you get all the mods. If its going to be a while I'd go ahead and get the tune first, then just get it tweaked later on. Up here the protuner only charges $160 to update the tune for new mods, and you're going to enjoy it the whole time, in addition to better gas mileage, responsiveness, cleaner burning engine, less wear on the spark plugs, etc.

If you like tinkering yourself pick up that tuner version that the guys selling in the classifieds for 600, have the protuner do a dyno tune for 300 or so (you'd only need the dyno time since the tuner version comes with the license) and then just go back into the tune and adjust the A/F yourself after you got more mods. winning all around