Last upgrade I did from 3.71 to 4.4 had the same symptoms. I edited AV, opp locking, looked at malware, added memory, tested cabling, replaced switch and manipulated connection speed. The biggest bang for my buck was changing 100MB NIC's to 1GB and adjusting AV exclusions. Also, disable shadow copy on the server if it's configured to run during business hours... and schedule server hard drive defrag (to run after hours).