Thank you all, here are some answers:
The first mod was putting on the new wheels and tires. Those made the biggest change in handling - it made it enjoyable to drive. I then added the 1" lift, but I used 4x4Cal's method of combining front spacers, LE front springs, SE struts and shocks, and custom firmer rear springs. So while it's higher, it also has the sportier dampening of the SE, so effects of the extra height are muted. I would say it handle slightly better than just adding the new tires, I almost dare say it is fun to drive.
Regarding costs, you prompted me to add it all up - ouch! So the van needed new struts, shocks and probably springs, brakes and tires - so that is probably a good $2500 that it needed in maintenance. But the total came to $6000. That includes a couple expensive mistakes on my part. It also includes a few improvements that weren't necessarily apart of lift modification, such as upgrading the horrible stock halogen headlights to awesome HIDs.
Yes, everyone we came across thought it was a stock package:
"Yo, someone's got an off-road minivan Bro!"
"Is that really a 4x4? I really wanted a minivan but I need 4wd."
"Dude, that van has the TRD 4x4 package! It's got the upgraded suspension and 4wd"
"That is exactly what I wanted! I hate driving that gas guzzling Sequoia"
"Hey Hun, remind me when we get home to research Sienna TRD"
For the custom exhaust, I took it the less safe part of town to a muffler shop that'll pretty much do anything you ask. They put on a Magnaflo single in dual out muffler and the dual pipes. I drove it around the block and pulled back in and told them to cut out the Magnaflo and put in the quietest thing they had. He used what he called a 'silencer', whatever that means, but it's a little louder than stock. Not too bad, has a nice little snarl from the outside, but at certain throttle positions it can drone a little louder than I like on the inside. See attached pics.