Dear Rose,
@1 I have seen your not about problems with compatibility. I understand that it is a common problem so maybe it is worth looking into it. Especially that modified cart/checkout is very desired option. are you aware of payment providers who are compatible with your theme? Stripe?
@2 Yes I use single product bulider, I have not tried without it. If I disable it will it reset the settings? As always this way of troubleshooting is well… troubling.
@3 as above. I have seen this issue on the forum before.
Please not – ability to provide variety of payment options (GPAy included), instant checkout is something which for eCommerce owner is one of the priorities.