They shouldn't rub w/a 3" BL, and only a little bit w/a 2"(may have to beat the body seam back some), it will depend on width of tire and backspacing of the rims you have.
You will have about a 18% loss of power, your speedo/mileage/mpg will be off by the the same 18%, so you will have to remember this when driving, i.e. if the speedo says 50mph, you are actually doing 59mph. You wont use 5th much, and your clutch will see a shorter life span. Mudding may also not be that fun, since you need to be able to spin the tires for them to clean themselves out. In the short term it should be livable.
Re-gearing wont be that expensive if you find a some 4.87 equipped oem diffs, they normally run about $200-250/diff. A set of 4.56 equipped diffs would be an improvement, there is only about a 7 diff between 31's and 33's, and the 4.56 gear set is oem for 31's, and are also usually easier to find since they came in more 3rd gen Toys(same gen as your '94). Factory 4.87's only came in automatic V-6 trucks and Runners that came stock w/31's, while the 4.56 gears came in trucks and Runners w/manual transmissions and stock 31's, but also came in trucks and runners w/V6 and auto transmissions. I am not sure which years, but my sisters '95 3.0 Runner w/auto had the 4.56 gears.
