I think the Clique losses are just variance. If they're hitting a 1-of with you unable to find a more-than-4-of to kill it you're just unlucky. Against Jace, Liliana is actually pretty good because she doesn't need to wait as long to ultimate and unless you're far behind already will be able to, at worst, Jace/Lands split them before Jace fires. Liliana + Jace or Liliana + Sylvan should just be game over for them unless you're dead on board. Them Entreating for a bunch of Angels can be problematic if you don't have Deluge main.

Preboard the most important things to do agianst Miracles are: don't go hellbent with Lili out, keep pressure on but don't overextend into Verdict or Terminus (DRS + Goyf is plenty), use Vision effectively, and don't waste Decays. Out of the sideboard you have incredible options against them if you need them: Maelstrom Pulse, Zur's Weirding, Null Rod, Krosan Grip, Notion Thief, additional copies of Sylvan Library are all great.