I would normally do the painting at this stage, then proceed as normal, unless of course you need to align the hand-painted markings with any of decals.
Regarding the paint bleeding at the masking tape edge; if you're using ordinary masking tape, then it's not so good for such scale work, better to use Tamiya tape, which has a sharp, thin edge, and can be burnished down tightly. However, with either type of tape, even when burnished, it often helps to seal the edge of the tape with the same colour being masked, as this will prevent the next colour bleeding through.