I would strongly advise against changing engines at this point, it will kill your momentum. Maybe try something new in a future project if you feel that SRPG Studio is too limiting for your ideas.
If features that you want to add seem difficult to implement than perhaps you could try a solution with stuff that you know how to do. When using a prebuilt engine it's usually best to take advantage of things that it's good at rather than morphing the whole thing into a something else entirely. Making characters strong against specific enemy types for example is something that should be very much in-tune with what SRPG Studio is great at. My suggestion for grayed out boxes could be done using picture popups instead of tinkering with menu code. Having the night scene start on the ally turn could also be done by applying a sleep status that prevents ally movement on that turn to the same effect. There's always more than one way to add a feature, and aligning your additions with the strengths of the engine will both reduce your workload and make the game experience feel smoother for the players.