The reason you don't have 4th gear is most likely the 4th gear hub shaft has stripped. This is common.

You can use a non-hd transmission if you have the gearing reprogrammed in your pcm. You can also use your HD parts in the new transmission. As long as you stay 98+ you should be good swapping parts. In 97 the diff/output shafter were slightly different.

If you used a non-hd trans with the HD diff, you'd have a 3.29 gear ratio.