As you have mentioned you are running a software business since Jan. 2018, ITR- 1 was not applicable to you as it was not an income from other sources. Either you could have filed ITR-3 or ITR-4.
Yes in current F.Y. 2020-21, you may file ITR under presumptive taxation scheme. We need to check whether section 44AD or 44ADA is applicable to you. If it is a software business, then 44AD is applicable. If you are providing IT services in professional independent capacity then 44ADA is applicable. Selection of correct section will depend on the facts.
1. Yes you are right
2. Yes you need to apply for GSTIN
3. Direct transfer will be more better than payment gateway.
Cryptocurrency is a virtual currency and not recognised as a capital asset under income tax act till date. Definition of capital asset is exhaustive. It may be treated as capital gain income or business income. You will get different views on this topic. It is better to treat such income as business income.