It won't really hurt the value because the stock auto box is rubbish. Many on here have converted to the stock 4 speed or a later 5 speed. Most switch to the later 5 speed because it either adds another intermediate gear (if you use the close-ratio dogleg box) or gives an overdrive gear for highway use is you use the OD box. Most use the OD box, as it is significantly stronger than the dogleg CR box.
There are many, many threads asking similar questions to yours, as a manual/5 speed swap is arguably one of the most common questions asked on this forum. Take a search around and you will likely find exactly what you want to know.
