When I bought my 4Runner I put some running boards on. First off I would say yes, you get quite a bit of extra ground clearance with them off. The 4Runner also has a more aggressive stance with them off. My Wife is 5'2" so I had to put them on. When I put them on, I basically bolted them on underneath with 22 16mm hex flange bolts at 20 ft/lbs of torque, (11 on each side). There is a palce to bolt them on, so you can put them back if needed.
The small problem you will have is the end plates. I had to drill a hole in the rear side wheel well and put a 5/8" screw, which you need to take off. When you take off the end plates, you will need to buy two front mud flaps for the front, but if you have wheel well molding you will have to buy front and back end plates that are not for running boards. In 2001 my end plates cost around $100 when I bought them on-line.
I kept my old mud flaps in case I decicde to change back to no running boards again.
