So, I finally got around to checking everything. No water in separator, no other glaring issues however I did find out that the choke was staying on longer than it should. Like it would choke for 2-3 minutes on a 70 degree day. So I readjusted that and suspect that could've been the issue. It very easily could have gotten knocked around while it was in the garage waiting for the rebuilt engine.
Anyway, I ran her very hard to duplicate the issue and then some and didn't get even a hiccup. Only other difference is it was 75 degrees out not 90. Time will tell but for now, I will say this is resolved.