It is "were going to" in each case. The first sentence does not make sense. You mean: ... I would be in now" or "I would have arranged to be in until tomorrow.". Needless to say, such sentences are also very uncommon.

Привет Евгений, Of the second pair, the first is certainly incorrect because of the wrong tense: "you are going to come yesterday" is impossible. The second sentence is completely correct. Of the first pair, technically I think that they both could be correct, but they are both a little clumsy. Probably better to say, "If I had known that you were (or are) going to come by tomorrow, I would have been in then." The "I would have been in then" implies "I would have intended to be in then," or "been sure to be in then," or "made it my business to be in then." These intentions, although in the future, precede the other person's coming. Relative to the other person's coming, they are in the past. Therefore, "would have." The choice of "were/are going to come" I think depends on whether you are shading the meaning to indicate that it was, or was and still is (if you know) the person's intention to come by tomorrow. Maybe he is coming to see someone else. I hope this helps. I think these nuances would be difficult also for some native speakers of English to grasp. Кстати, я пытаюсь нацчиться говорить по-русски. George

Anna, thanks a lot for your detailed explanation!! "If I had known you were going to come by tomorrow," unless it is already sure you couldn't be there. I think that's the case. I took it from this site: https://www.englisch-hilfen.de/en/grammar/mixed_conditionals.htm

It is "were going" because you used "if I had known." You are talking about something that did not happen and explaining what would have happened if things were different. If I had known you were going to come by yesterday, I would have been home. If I were going to the circus, I would want to see the tigers. You can't say, "If I had known you were going to come by tomorrow," unless it is already sure you couldn't be there. Yes - If I had known you were going to come by tomorrow, I would not have gone on a trip. (You already went on a trip and it’s too late to change your plans.) No - if I had known you were going to come by tomorrow, I would have answered the door. (You still could answer the door tomorrow.)

This is the 3rd conditional (nothing should be in the present) - http://www.perfect-english-grammar.com/third-conditional.html