Like all of the others, I would do it all at once. I went through the same thing as you, hated the way stock ride looked. Went through all of the options (Spacers, Bilstien 5100, coilovers and springs). I saved up and went with Toytec coilovers, springs and UCA's, couldn't be happier.
That being said, if I could do it over again I would've went with icons, don't get me wrong I like the ride quality of the Toytec's but they are a major pain in the a$$ to adjust being bottom adjust coilovers.
Good luck and remember, buy once cry once.....
-J
Thanks for posting this thread and comment up. I, too, am going through this debate in my head. Biggest thing is there's sooo/too many options it just gets a bit confusing. I too first looked at spacers but shot that down. Then on to Bilsteins with stock springs. Current progression is a conglomerate of Toytec, Boss, and Icon. Shurg.....
For example, I have a 2013 TE and if I went with Icon....
Icon Stage 1, standard travel, $1,754.80
2010 5th Gen 4Runner Stage 1 Lift - Metal Tech 4x4
For $325 more add in some UCA's
Icon Stage 2, long travel w/ LR UCA $2,079.80
2010 5th Gen 4Runner Stage 2 Lift w/ Light Racing UCA's
For $930 more change the UCA's to billet. (Really?? Are billet $930 better? Not sure.)
Icon Stage 2, long travel w/ billet UCA $3,009.75
2010+ 5th Gen 4Runner Stage 2 Lift - Metal Tech
Of course there's these options too:
Bilstein w/ FJ $909.99:
3" Lift W/ Bilstein 5100 Height Adj Coilovers FJ/4Runner
Toytec Ultimate $1,218.99:
FJ Cruiser/4Runner Ultimate 3" lift package
Boss $1,259.99:
BOSS Suspension System for 10+ 4Runner and FJ
Add another ~$1000+ for 285 70 17 tires on stock rims (should fit with any of the above I gather).
Perhaps I just need to spreadsheet this up and look at how they compare. I'm also totally open to listening to suggestions for things I know I'm overlooking. I come from motorcycle background, not cars/trucks. I love getting out, exploring, and being a bit dumb in some people's mind - yes I've had my old WRX on 3 wheels loaded in Mexico on high clearance roads. It's all about picking a line

I'm loving my TE and know in the future I'd like to beef my current ride up a bit both for aesthetics and potential clearance issues.