For whatever reason, the way I put this into my calculator was dumb and I got (2) X Rails of 56.625” and (1) Y Rail of 36.125”.
Looking at this now, it seems kind of stupid, but I’ve already cut my conduit and my belts. Should I fix it now before trying to go any further or will having a long X axis than Y axis be okay?
I also made my table exactly 61.5 x 38.375.
It won’t hurt anything except cut capacity. Your long cuts will be on the X axis. I think it would be better the other way around for rigidity. I mean you would only need to cut one of the rails down. But you will be fine.
Ideally yes, the X gantry is only supported on the edges so the shorter it is the more solid it will be compared to Y which will be fully supported by the table.
That being said there are a lot of us here that use 4’x8’ tables without issues.
It is up to you based on your use case, space availability, and ideal X vs Y . I have seen others on here with a longer Y though. If you can change it I personally would though.
One thing to consider is that with the way you have it now there is potentially an advantage in that you can still load full sheets in the machine, and if you want you can make longer cuts by tiling in cam and then sliding the sheet.
I’ve always had it that way because I wanted the better access more than the bit of rigidity I lost. It’s not suggested though. 
For my first time, I went ahead and flipped it back around… I had enough conduit left thankfully, and I hadn’t fully assembled yet. I just need to cut and feed the belts again now. 
