This might be a stretch (no pun intended), but let me know if my theory is valid?

I use a Specialized Phenom in 143. I've been getting knee pain recently, and it's not my saddle height or cleat position since I haven't changed those. I have been riding more frequently and notice that my hamstrings are hurting. I think because they are hitting the edge of the saddle. Could this in turn cause my hamstrings to pull on my knees, causing pain?

Try a different saddle and find out.

or...push your saddle back a bit and ride it more forward taking pressure off of the inner thighs. This position may not support your sit bones but you may find it provides relief. Saddle tilt matters as well. Other factor is left to right symmetry...some benefit from canting the saddle slightly left or right...I do for example.
Good luck.

On the Toupe shaped saddles I find sitting forward puts pressure on the soft tissue. I'll try another saddle. I was thinking knee pain meant saddle height or setback issues, but it could just be 143 is too wide!

I found when riding a toupe I tend to sit further back on the saddle than with other saddles. You probably need to lower your saddle to get the same position you had before.
If your thighs are hitting the edge of the saddle you probably have it too high. I used to have this problem but have slowly lowered my saddle a lot and moved it all the way back with a set back seatpost. If you look at pros bikes they almost all use a low, very set back position on the bike.

I believe saddle width is a balance bewteen supporting your sit bones and yet having enough relief to not encumber the pedal stroke....a balance in other words. So shape matters a fair amount. In the case of the Toupe shape...the thigh edge is pretty sharp...so maybe affecting you. A suggestion if purchasing another saddle is consider the Romin EVO. It is more curved side to side and hence friendlier on the inner/lower thighs.
In the short term, try lowering the saddle a bit...and playing with the tilt.
Good luck.

It is a balance. I think all of bike fitting is a balance. But, if my saddle height is set perfectly
now, lowering it to compensate for the saddle back being too wide doesn't work.

I'll try my Rolls tomorrow, to see if that helps.But it does seem a different shaped saddle is needed!

Anyone know if the narrower Toupe 130 saddle has more thigh clearance than the 143 size?