1 ) 我想你了is natural and native.
2 ) 我已经想你and我想过你了are unnatual in that context.
3 ) 我想你了is in the present tense. 我已经想你is in the present tense, or in the past perfect tense. If you add in "现在"as"我现在已经想你", then it's in the present tense, by the way, unnatual. If you add in "刚才"as"我刚才已经想你", then it's in the present tense, by the way, unnatual,too.
4 ) And same for 我想过你了, which is unnatural and weird. If you delete了as 我想过你, it can be used when your girl friend or someone else asks you whether you have thought of her or him when you were on a break, I mean after a quarrel. If you say that, you really like her or him though you have some problems with each other.