On the Toyota front axle, the driver side spring perch sits lower than the passenger side perch. The stock driver side spring has more arc to make up the difference. when using aftermarket lift springs or RUF, the spacer (3/8 I believe) is used to make up the difference, so the truck sits level.  Are you using bump stops? Is it possible that one of your four springs is bent/sagging, front or rear ?
As for the shims, it's really hard to say without seeing your setup. When it comes to front shims, they are generally used to correct caster more so than drive line angle. Depending on whats been done to your truck the shims may be installed correctly. How is your steering? I would pull the shims out and test drive it. If it drives the same or better leave them out, if worse put them back as they where.

Cheesemaker, you left out the best reason people use RUF, they flat out work
 Ruf are not as straight forward as store bought lift springs, but when put together right and properly tuned RUF can be what ever you need them to be.