No, you can't use 3 & 4 and maintain 16x speed for both. You said you will be using 2 & 4 and it would be OK for 16x/16x.
You can use 1&3 or 1&4 or 2&3 or 2&4 to keep it at 16x/16x, and not 1&2 or 3&4 as it will drop to 8x/8x.
About using x1 card by the side of VGA and maintaining VGA at 16x, I'm 99% sure, as I read it somewhere what people tried, but didn't try it myself.