Different types of subjunctive

No.

1 is never seen
2 is the usual
3 is never seen

"had done" is a phrasal verb meaning "finished with" and is not to be considered a guide to using the subjunctive.

Well, they are correct although they can be found in Old English. You just never realized that they are there. Check these out (perfect subjunctive)

......accursed hound is to return to the city to-night, it is high time he had left the shore." , Suddenly the man at the masthead announced a sail in sight. (by William Lightfoot Visscher)

Now the rich merchant deep in last weeks papers thrown aside till sunday — is reminded by his better half that it is high time he had dressed for church — most willingly would he give the church the go by......

It is high time they had come to treat those who differ from them in matters of .......(Watchman)


Present Subjunctive

I wish I be not now proud indeed ! (by James Ballantyne - 1824)

To say that they are not correct is not correct. They are not used anymore but are correct.

If you know so much, why ask here?

The answer is in my question.

1) Is the first construction with the perfect subjunctive relatively often used in your place?

2) The second question depended on the answer to come.