The Volpe is a great bike. The going rate for them here is $850 at all shops, so $950 sounds high to me. That would add another $100 to your pile-o-cash. Keep in mind any sales tax that might eat into your math.

Best thing to do with the extra cash is to put it someplace safe until you need/want something vs. burning it right away.

But, if you must...

Clothing is always a good way to go. Long sleeve jersey, SmartWool socks, cycle shorts, etc. I personally like the HI-VIS color shirts/jerseys since I commute in traffic.

The tools you mentioned didn't include cone wrenches or a chain cleaner. You're going to overhaul your hubs most often as the headset and bottom bracket are sealed or semi-sealed. Get two of the same size you need.

The Deore deraileur is very good, I wouldn't upgrade until it needs replacing.

A rigid seatpost would be a worthwhile investment.

One LBS told me that almost every Volpe they sell goes out the door with 28mm road tires on it. I actually did the same thing to the Kona Jake I chose.