I'm rebuilding a 06 GS500F engine, I have a 89 to 97 Haynes manual and everything seems the same , are there any known engine spec changes from 97 to 06 engine?

Others on the forum are more knowledgeable than I, but I'll get it started.  The camshafts are slightly different due to eliminating the mechanical tachometer drive and camshaft end-play.  Carbs are different, as well as the ignition box.

Specs, torques, and clearances should all be the same for the internal mecahnical stuff. There will be some missing torques values for newer items like the oil cooler lines, but use a similar fastener's value. Most torque values in an aluminum block will not be much.

Not much major changed, just mostly the carbs as mentioned earlier, your floats look way different and jets and slightly moved, so just go to http://www.bikebandit.com/2006-suzuki-motorcycle-gs500f/o/m9752 for up to date info

The routing of oil is different on the bikes with oil-coolers.  Not sure how that affects the rebuilding process...if at all.

That's good I wanted to be sure bearing shell codes, clearances and torque values hadn't changed. The engines #2 rod bearing was bad, I was lucky to find a NIB Crankshaft and rod bearings that someone ordered and put a deposit on the parts at a dealer, the guy backed out of the rebuid so the dealer sold me the Crank, Bearings, generator Rotor all OEM new for $150. I'm waiting for gaskets, 1 rod, rings and misc parts so I can reassemble it. Parts cleaning next. Thank's for info.