I might try the wheel swap technique. After giving it some thought, I think I know what was going on: Whatever minor differences I perceived in handling were likely a result of:
FIT - I didn't fit either bike to me before I rode them. The Pinarello is the sellers personal bike and was setup for him, the Colnago was a bike his brother just gave him that had been sitting in storage. The saddle on the Pinarello (a modern Serfas), felt better and gave more positive control than the one on the 'Nago, (an Avocet).
TUNING/PARTS - The Colnago needs a tune-up. Part of the reason the Pinarello felt so good, probably had to do with the fact that it was in exquisite working order and had better parts (irrelevant, since I will be building it with a modern group). The full Super Record group with Simplex Retrofriction shifters, (that combination is, without a doubt, the smoooooooothest shifting I've ever experienced), and C-record hubs laced to Wolber clinchers WITH high quality tires (Vredestein Fortezza) probably made up for the rest of the difference between the two bikes.
Case in point:
When I customized my Univega (again):
I changed the groupset to new Ultegra, got a new seatpost, new Deda cockpit, different wheels, and changed nearly every part except the frameset. When I took it on my first few rides, I seemed to have a different level of control over the bike. I couldn't seem to corner as sharply, I felt slower and heavier, and I felt uneasy doing fast runs on downhill runs that I normally felt pretty comfortable on and often rode very aggressively on.
The fit was good. I wasn't getting any pain or discomfort. It just felt off... maybe it was the wrong size for me. Discouraged, I thought about selling the bike and getting something different.
Then one day, I decided to play with the fit some more... I don't remember what I did, but you know what? It cured it! Immediately, the bike fit me perfect, I felt comfortable and confident at all speeds, the bike cornered like a demon, and the new parts, (especially the cockpit), made a noticeable improvement. I couldn't be happier with the setup on that bike, (except for the wheels), for all around riding/racing. Now I just want something a little twitchier than the geometry of the Super Strada frame will ever really allow...
After having thought about it: I'm confident that this Colnago will do what I want it to do, probably even better than the Pinarello. Best of all, I wont have to feel guilty, in any way, for personalizing it to meet my expectations (Shimano group, modern componentry, etc.)