If you're trying to using the stick instead of the dpad, that's probably why. If you're already using dpad, I don't know what to tell you. Just practise. A lot.
The problem with 46P in strings isn't the actual 46 motion. It's the timing. It can't be mashed. You have to actually time it with the punch before it's suppose to come out. Once you have the timing down, it should be free. And it's not that big of a deal, honestly. It's just a tiny damage improvement.
As for instant FC 3P, you can do 663P or 623P during the animation of the move before it. So do a launcher, and then see about doing those FC 3Ps. A simple combo is CH 8K FC3P FC3P 3PPP~46P. Remember to buffer the 663 or 623 motions during the last move so your FC3P comes out as fast as possible.