Gary, when folks talk about rod clearance they're usually reffering to the big end of the rod. The simplest way to do that is with plastigauge. You can get it at your local auto parts store and what is is a string of soft plastic that you place on the crank journal. You then install the rod torquing the rod cap to the manufacturers spec. You then remove the cap and measure the plastic by comparing it to the marks printed on the package. When you install the rod it squeezes the plastic. It is pretty accurate and is a very cheap way. You're looking for at least .0015 to .003. If you have more you might consider using at least a 30w oil.
The piston to cylinder wall clearance is measured by measuring the piston at the skirt perpendicular to the wrist pin where the piston is the widest. You then lock your dial caliper (or micrometer) at that measurement and zero a dial bore guage in the dial caliper. Then you place the dial bore guage in the cylinder also measuring primarily at the perpendicular to the pin. The dial bore guage will read the difference and you're looking for .002 to .004 depending on what your intent with the motor is. You may consider the bore finish, rpm range, intended oil, life expectancy, piston type (cast, forged, hypereutectic), ring type, fuel, etc. You can also use the dial bore guage to check bore taper and out of round. Randy has a lot more experience with this and I'm sure he can tell you better specs for stock clones.
