on a straight-to-end run, you could get rid of the blue shell after 8-3, and from there you could keep going with whatever (of course you need to get the star power). and a faster way to beat masked bowser jr. in the towers is to jump on him, then to a ground pound on him since a ground pound counts as two jumps on the head, then on the right frame, before mario automatically turns to the player for the victory pose, you could turn to the left/right (depending which way you're facing) to get out of the tower faster and save a frame or two.
Another thing is to make sure that you defeat Bowser Jr. as far to the right as possible, because when he jumps out after you defeat him, it takes out a load of frames.
I found this speed trick with a mega mushroom (which can be seen on
my level 1-1 freerun )in which you ground pound on a slope and jump immediatly and continue jumping. it's similar to the hoping glitch in SMW. however, i tried it with the other variations of mario, and they didn't seem to work...