I'm assuming that you will be driving the x axis with the same gear rack? With the same motor and gears and gear reducers? Might as well keep it simple. Use the same drive on the y axis. That looks like a fairly long machine, so I assume that you are using gear rack on the x?
So this is a suggestion:
IF you have space for the gear rack on the face. Otherwise you'd have to put it on top.
That looks like a mighty large circumference of threaded rod with a very fine pitch. Without knowing the details and specifics of the whole design including gear ratios, motor graphs, threaded rod pitch, efficiency of threaded rod, etc, etc, I can't give you too much advice, but I do suspect that if you are using gear rack on the long axis, you definitely want to use it on the y. Otherwise you could end up with a speed mismatch of the two axis, and you'd have to go with the slower speed for the overall speed. Also, I think it will be easier to make circles round, etc, when you are cutting if you use the same things that will have the same amount of error on x and y.