I've not been able to install a fork seal into the lower, then install the upper through it, without deforming it and eventually causing a leak.
Which in the end means I had to remove the whole fork from the tree, with the seal removed from the lower, install the upper into the lower, then slide the seal down the entire length of the upper and seat it into the lower. Guaranteed no chance of deforming the lips this way.
Like Johnny said, check your bushings. Also suggest you get some gaiters to put on it at the same time as well, keeps the bugs rocks off the uppers. Rancho 1952's are a popular option.