I found a copy of Afikei Yam of Rabbi Yitzchak Isaac Chaver, which is a commentary on Shas, according to Pshat and Sod.
There is much written on Perek Chelek, and perhaps I'll get to it later. Here's a short bit regarding the hours of the sixth day from Sanhedrin 38b:
אמר ר' יוחנן שתים עשרה שעות היו היום וכו' - מאמר זה ביארו רבינו בפי' לס"ד פ"ה ובו מבואר קץ של משיח שהוא יום ששי נגד אלף הששי שבו ממשלת אדם כמ"ש וארו עם ענני שמיא כבר אינש אתי וכו' יעו"ש, וסדר השעות, ומשכם ובין כל דבר בעתו ובזמנו, ואין לגלות אלא מפה לאוזן שומעת
Rabbi Yochanan said: There are twelve hours in the day etc - This section was explained by our Rabbi (the GR"A) in his commentary to Sifra diTzniuta chapter 5, in it it is explained the Keitz of Moshiach, which is on the sixth day, paralleling the sixth millennium, in it the government of Man, as it says (in Daniel chapter 7): "And behold he came with the clouds of heaven... ", see there in depth, and the order of the hours, their duration, and among every matter in its hour and time, and it is not to be revealed except from mouth to a listening ear.