The automation of Network Services (NS) consisting of virtual functions connected through a multilayer packet-overoptical network requires predictable Quality of Service (QoS) performance, measured in terms of throughput and latency, to allow making proactive decisions. QoS is typically guaranteed by overprovisioning capacity dedicated to the NS, which increases costs for customers and network operators, especially when the traffic generated by the users and/or the virtual functions highly varies over the time. This paper presents the PILOT methodology for modeling the performance of connectivity services during commissioning testing in terms of throughput and latency. Benefits are double: first, an accurate perconnection model allows operators to better operate their networks and reduce the need for overprovisioning; and second, customers can tune their applications to the performance characteristics of the connectivity. PILOT runs in a sandbox domain and constructs a scenario where an efficient traffic flow simulation environment, based on the CURSA-SQ model, is used to generate large amounts of data for Machine Learning (ML) model training and validation. The simulation scenario is tuned using real measurements of the connection (including throughput and latency) obtained from a set of active probes in the operator network. PILOT has been experimentally validated on a distributed testbed connecting UPC and Telefónica premises.