shortening the cables is easy, especially the clutch cable.
the key is to cut the outer sheath and then cap the end of the sheath with a cable end. you can get crimp on cable ends if you buy a pack of new bike cables. But, it's like $10.00 for a cheap set of cables, and that's $10.00 spent just to get the cable ends.
shortening the throttle cable isn't that easy because you have to cut off the end that mounts the cable into the throttle. then you have to make a new end with silver solder.
It's not that big of a deal to do it, but you have to know what you're going to do before you actually do it.
I had to shorten my cables because my bikes are only 20" ers, and they both have really low bars.
yes, you can add more fuel line and you can make it a loop, but make sure that it's a smooth loop with no kinks. your line right now might be ok if you shorten it just enough to get the kink out of it. as long as fuel flows though it. it might be ok as it is. I think i'd try it and see how it works as it is and then change it later if it's a problem. OR, loosen your gas tank and slide it forward until the kink in the line is gone.
you can buy an actual one peice off-set intake manifold rather than trying to make one.
the thing that might happen is that the epoxy might break down over time and give you an air leak which will make your engine run lean. you may experience problems getting it to idle, and it may develop a bog when you open the throttle all the way.
the epoxy may last for awhile as it is, but you never know.
or it may fail, giving you an air leak or making your carb fall off while you're riding. there's a lot of vibrations there, and extending the manifold magnifies the vibrations.