You need to lift the front some. If you leave the weight on the front wheel and remove the upper support it causes the lower to twist a small amount because its now trying to rotate. the bike should be lifted to the point that the front wheel is just bairly touching the ground.
One of these days someone is going to snap a lower tripple because they removed the upper with no support under the bike..........they are designed to break/bend during a front impact to help lessen the amount of energy transfered to the chassis. Sorry for the rant..........it just seems there have been a few topics here lately with people asking the same questions regarding the upper tripple.