If the knot is good sound solid wood, just leave it, otherwise drill it out, ream back to sound wood and glue in a plug.
A slightly stiff handle on a longbow is OK.
A knot going through the centre of the limb will be ok, just leave a tiny bit of eatra wood round it, Yew is
very forgiving.
Look at the pics on my website, I deliberately made a 'bad' Yew bow with a horrible knot in the centre of one limb with no extra left round it and it was fine, also my fave' longbow has a huge knot in the handle.
(Click on the globe symbol under my username) The 'Yew Longbows' and 'Other Yew Bows' pages will be of interest.
Cross section of longbows from the Mary Rose varied from almost circular to almost square, I like a rounded belly and a flatter back following the surface of the underbark or a growth ring.
If you want it to look like a longbow don't shorten the stave at all, 69" is a nice length, I see too many people with longbows taller than themselves, and conversely some people think an ELB can be 60"
Del