long to short tailshaft swap question

The 18t O/D gear will not mesh with a cluster from a 20T ratio; so you are OK on that front.

There are several sources of noise. Some internal and some external. Also EP oil muffles internal noises while a synthetic will not. It behooves you to figure out where the noise is coming from, on account of it could be a cheap fix or not.
On that note;
Is the noise in all gears, or all the time or just in a specific gear or in neutral. Is it noisy in direct gear (third)? Does it change when the pedal is depressed? Does it change with power application to compression braking. Is the noise accompanied with vibration.
If you don't figure it out, you may just end up back to square one, with a swapped over tranny.
The cluster-pins as mentioned, like to wear. I have flipped them over upside down and cut a new groove in them for the woodruff. Then they can go for many more miles. I have also bushed the front cluster hole to be a light press-fit.
Take it easy when shifting into O/D; I have zipped the teeth off a couple of those 18Toothers, and it didn't take much.