Have the eye doctor evert (flip) the upper lids, to look
for a condition called GPC, or
Giant Papillary Conjunctivitis. This is an inflammatory reaction to the contact lens and proteins on it, and can cause some of the symptoms you are having. Treatment consists of a period of no lens wear, a combination anti-histamine and mast cell stabilizer eye drop, and possibly changing to gas permeable or daily disposable soft lenses.