xcmark,
Great Questions regarding the Dynojet line of fuel control products. Your decision between Fuel Only or Fuel + Ignition is entirely up to you of how much control you desire. I've seen excellent results when tuning with the fuel only unit, and really seen machines come alive using the F/I units especially when port timing and exhaust cross section have been altered.
Since you're already interested in the POD-300 Digital Display, rounding out the system with an Autotune/WB2 unit is an excellent choice as opposed to the separate meter system. The AT uses the same Bosch LSU 4.2 sensor, and is pairable with all Dynojet fuel controllers. The AFR value can be displayed live on the POD-300 as well as activate the autotuning feature which will automatically adjust trims as you ride to hold a target AFR - which isn't possible when trying to pair the PCV with a separate gauge/monitor such as a KOSO.
As for tuning guidelines, the same schools of thought that applied in the old days still are relevant now....Plug color, wash and wet line in the pipe are the most solid indications of what is going on inside your engine. As mentioned, EGT's can read low and you'll be extra lean, or hot....same is true on the rich side, but examining the conditions inside of the engine can't lie. AFR meters are much more dependable for producing an accurate representation, but the number on the gauge still must be correlated to the condition inside the engine.
~T.J.