Review time after third submission
I do not see anything unusual or particularly alarming in this situation. Your first review arrived very quickly &mdash; compared to Mathematics, where a first review can take 15-18 months in some journals. 

It is not unusual for reviewers to make remarks which appear contradictory. Sometimes it is possible to find a compromise to pacify both; sometimes (as in your case) it is necessary to rebut the criticism. Rebuttals are never easy and the suggestion of the first reviewer to reject a paper is not completely unexpected. Now the decision falls on the Editor, who has to either side with you (and potentially lose their Journal the Reviewer One) or side with Reviewer One and reject your paper. It is not an easy decision, and it requires for Editor to personally read the paper, or to invite another reviewer to join the fun. Whatever they are doing, three months does not seem overly long yet to me.

tl;dr: It's best to wait patiently.