Based on your description, it sounds like the resin isn't actually sticking to the build plate. The FEP material is really really non-stick and nothing should really cause it to degrade chemically either. So your ammonia based cleaner is fine for the FEP, though it's really bad for the acrylic. So avoid using it there. And no, there isn't a good side and a bad side or anything. Both sides are created equal as it's the same material all the way through.
I would try increasing your first layer cure time to something ridiculous like 30-40 seconds. Because you are using FEP there's no risk of burning or degradation. So any initial overcure will just help cement the part to the build plate. Your peel seems fine or could even be considered slow. Once you overcome this issue I would try increasing a slight amount depending on how large the part you're printing is. Personally I use about 1-2mm/s for the first 30-80 layers, then I switch to 12mm/s and it cuts printing time way down.
On my home lab machine and MakerJuice SubSF Red, I have 10 second layers, and a 60 second initial 2 layers. It's a huge number but the parts are always stuck to the build plate!
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