It's no secret, Les.
The wood stains because it isn't sealed, so you need to seal the area around the crack before applying high viscosity CA glue. What you intend to do with the piece afterwards has an influence on how you seal...so if you're going to colour it then sanding sealer, if oil/wax then you can seal around the crack with a finger dipped in oil and wipe around the crack. Apply thin CA so it wicks into the crack. Quickly wipe the top CA away with a rag. Fill crack with very fine dust...same colour as wood if you have it. Spray with CA activator. 400g rub down and repeat if required.
Then when you abrade the whole vessel the staining should minimal at worst.
If there are LOTS of cracks, as there were with this piece, I also "wash" the inside of the vessel with 60/40 PVA & WATER to seal the inner cracks.
And remember...Yew is VERY susceptible to heat checking from over zealous abrading. So abrade slow and keep the cloth moving, stop after every grade to let the vessel cool.