Yes; 4.125"x4.00" is commonly referred to as "all bore" because all the displacement increase comes from the increase in bore diameter; very "torquey" motor. I was quite happy with that motor but when you go to the trouble to split the cases for the case bore, particularly if having the crank addressed, i.e., T/B/W, why not stroke? It just makes sense to stroke the motor as well to 117" or 124". As much as I liked that motor, I would not split 88" cases again and stop af 107". The additional cost is marginal but the increase in performance is a step change.
High TQ/HP are the result of heads, cams and exhaust playing well together but, as you know, those are peak numbers. A good tuner is necessary to pull it all together to get peak performance at partial throttle where we ride. Most are afraid of higher compression but should not be. The 98" motor referenced in my last post is set up at 11.2 static with CCP at 212psi. The all bore 107" motor was set up at 10.4 static with CCP at 197psi; I ran 87 octane at the compression level and made the TQ/HP number previously posted. Gotta get the right parts but the tune is where it's at.
Smart to pass on the '01 EFI bike; you would be stuck with that MM system and carb conversions were a little more complicated then.