Elevated E2 levels will decrease your libido, absolutely. 90+ is a problem that needs to be remedied or else you will not see the results from therapy you are expecting.
The probable reason the shoulder area became less consistent is because the skin toughens. When I was on gel I experienced this. After a period of time, the skin on your shoulder area will become almost scaly, and the absorption rate will not be as consistent -- hence problems.
Why not switch to injectables?