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I have a early model 2900S from about 1981. It plays beautifully and freely. When the Bb concert is tuned properly the middle of the range tends to be sharp so I tune the Bb a little low and the rest are very close. 1st valve is typically sharp.

What are your experiences with your Willson's?

I think the throat of your mouthpiece is too small. Enlarging the throat of the mouthpiece pulls the high and low ranges sharper and should help to balance your intonation. Find a place with a good selection of pieces and a tuner and see if you can find a better match.

With Bb tuned low for the other pitches, the A sits very low. If there were a way to trim the 2nd slide a hair, I'd have it done in a heartbeat.
The horn has a 2950 leadpipe and receiver (bass shank), and I use a Schilke 51d.
The characteristics don't change much, if any, with other mouthpieces, but admittedly, the ones I've tried have all been similar (Schilke 52d, Kelly51, GW Kadja), and my euphonium chops are pretty stale.

All valve instruments are compromises. I have a slightly younger 2900. As long as the general profile is moderate, YOU are the only source of a good pitch. As an instrument pitched in Bb, the manufacturer will tend to construct it to favor that side of the circle of fifths. The low 2nd valve is desirable as most notes in its overtone series will function as leading tones, and low is desirable.

Look at my post on the temperament discussion.