All very good.
One way to make things easier is to realise you don’t have to cold solve every clue before encryption and grid entry; once you know enough of the mapping to work out which letters map to one and which to two, you can enter them into a sacrificial unencrypted grid, as either single letters, or C1 and C2.
With crosses, you’ll find that H1=F2=I etc, making completing this grid much easier, with the whole thing being back-finished by looking at viable possibilities generated for the encrypted one.