The Sterilgarda Go Eleven rider set a 1min 34.265secs with a qualifying tyre on Thursday, which DF Honda rider Muggeridge eventually beat by just 0.013secs at the end of day two.
Xaus didn't test on Friday due to a shortage of engine parts - many components having only recently arrived back from Australia – but Ruben thanked his team for the chance to at least gain some track time ahead of the April 4-6 Valencia race weekend.
The Spaniard won race one of his home round last season, but - despite his strong test showing - claims to be worried by the straight-line speed of the four-cylinders, which the Sterilgarda team says were 10 km/h quicker than the (non-factory) 1098s present at the test.
"Testing have gone really well although I'm pretty worried about the race," said Xaus. "I would like to win again on this track as I did the last year when I achieved my first victory with the team Sterilgarda Go Eleven. That's why we chose to take to the track for one day at least, although we didn't have all the equipment.
"Anyway we did a good job and we got everything ready for my home-round. I would like to thank all the team: the guys worked non-stop since the Australian round in order to give me the opportunity to be on the bike here at Valencia," he added.
"Unfortunately the machines returned to Italy just a few days ago - after the Qatar and Australian rounds - and we had to send many components for service in order to get everything ready for the next race on this track on the 6th of April," explained team manager Marco Borciani.
"Ruben confirmed his great moment both using the race tyres [1min 35.2secs] and the qualifiers. In spite of that I'm pretty worried about the gap from the four-cylinders. In particular I was stuck with a lap where Ruben was just behind Nakatomi. Although he was lapping two seconds faster than him, going into the straight with more power, Ruben could not pass the Japanese rider. Valencia is a strange track with lack of places to pass," he revealed.
Xaus is currently third in the WSBK championship standings, after round two of 14.
Team-mate Max Biaggi wasn't present at the test, since he is still recovering from a broken wrist sustained at Phillip Island.
