I did exactly the same as above, basically removing just the glass from the sides and top of the stringer.. I left about 1/4" of glass where it meets the hull and the stringer or what was left of it still in place.
made measurements from that (which will give you a rough profile) hull to engine mount dimensions being the critical ones although my mounts are height adjustable anyway.
I then carefully removed the last 1/4" of glass to hull/stringer very carefully with a metal sanding (not cutting disc) and lifted both the stringers out in one piece..
the front foot or so of mine was pretty much just mushy timber but its surprising that once the glass is carefully removed how much you will save for a template..
with the stringers removed what I was left with was a small upstand of glass where the stringer had been and this outline remains in the hull even when it was ground back to clean up the entire hull floor.
With a template (old stringer) to work off and an outline on the hull floor of the position the new one needed to go back in I found it quite straight forward to profile and position.
Last night was the first time I had both new stringers back in the hull and they're in perfect position and also level..
Best advice I could give would be take your time, take care with the removal and it'll save loads of headaches later..