longtravel project ......commence!

Sweet!! You've got a heck of a project ahead of you but from everything I hear you'll be VERY happy with the payoff!

I can't imagine why you wouldn't be able to go in stages like you mention. I believe the long-travel kit requires coil-overs with 8" of travel. If the 'hoes have that covered, they'll work as both a short-term solution for lifting the front and for your future plans. Lifting the rear is cake so don't sweat that.

Expect to spend a decent amount of time in the alignment shop since you'll be altering the suspension geometry multiple times. Just something to factor in when estimating total cost for the project.

Don't forget the cost of fenders and paint in your project. Most LT guys run these:
http://www.glassworksunlimited.com/shop/product.php?productid=81&cat=22&page=1

You should also head over to ttora.com and SEARCH. Seriously, search the hell out of that site before posting anything. We're a fun, knowledgeable, helpful bunch around here. They are too but they won't hesitate to rip your virtual head off for asking a question that's already been answered elsewhere.

Some serious rigs on that site, and there's a whole section dedicated to LT suspensions: Good luck with your build! Keep us posted on the progress, and as always, post pictures!