You should probably research the manual transmissions available and choose one before making the other choices.
If you replace the bellhousing crossmember with one from a '54/'55 1st truck its then easy to swap in the bellhousing from a late 50's V-8 powered truck, making it simple to mount most GM manual transmissions behind a V-8 in your truck.
But I know almost nothing about the 90's 5-speeds and you'll want to be sure it will work with one before doing all the work.
