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.

Actually in China, the second or the third are not traditional ones, though might be correct in gramma. Well referring to your doubts,: 了，已经，过。 They could be used in past tense, but in different context. Eg: I have missed u a lot, you could use 我想你了，it could be explained not only in the past, until this moment I am still missing u. 已经 could be used in the stentence that u wanna state that what u did, sometimes it underlines the verb used in the sentence. eg. I have asked this question on italki 我已经在italki上提问了，过 is smilar to 已经 but more like oral English, not offical one, could be used following the verb. eg: Have u had breakfast? 我吃过了。

第二句，不对，一般不会这样说。The second sentence is not correct. 但可以说：我已经想到你了。但和另外两句中的“想”的意思有所不同。比如说，你有两个苹果想送人，时，你首先想到了你的姐姐（想给你姐姐），也许还想到了你的朋友（他已经很久没有吃苹果了，也许给他比较好）。

In this case use the adverb: 一直 我一直好想你。 I haven't heard this one before though. Maybe no one misses me. Ha! BTW, do not think in terms of tenses in Chinese. They make no sense at all.

I think these is no tense in Chinese.