I think you are ok.
now that you have the bolt off take the nut off the bolt.
clean the head area and the manifold surface good.
someone else will chime in here with more and better info,
but, I think you should put some type sealer on bolt, then buy all new nuts for you manifold bolts. some may recommend buying all new bolts
I just did this to my little ferguson last year and I can not remember, I know I got all new nuts, but bolts I do not remember.
note to file: the threads Stretch, no kidding, so that is why you need new connectors. I would use two nuts locked together as you tighten the bolt back into the head.
as you have cleaned the threads, you should have no problems getting the double nuts loose and off.
some tractors use thick flat washers against the manifold then the nut, some may use a flat washer, lock washer then the nut,
but the main thing is to torque the manifold nuts down to the correct pounds per sq in. you will need a good quality torque wrench. use a varied mixed pattern as you tighten the bolts. these items may be elementary to you, if so please disrequard, but serious mistakes can be made tightening bolts attached to the head, it's not like tightening bolts on an old plow or disc.