I recently replaced a pair of Cane Creek SCR-5 levers with new 9-speed Shimano Sora STI shifters. After the swap, it feels like there is no modulation, especially on the rear.

With the old levers, I could scrub a little speed with just a touch of the lever and never had to worry about locking up the rear wheel. Now I have to really squeeze the lever to scrub and if I go just a tad further, the wheel locks up. There's no middle ground, it's weird.

Calipers are 105 BR-5501 and cables/housing are brand new.

So I'm wondering if Shimano changed the cable pull with this group? Maybe I just need to get used to the new ergonomics?

According to Shimano's spec sheets (2016-2017 SHIMANO Product Information Web) both the 3500-series and the R3000 series Sora levers use the "New Super SLR" cable pull standard. The 5501 brakes would be the old "Super SLR". There isn't a lot of difference between them, but there is some. The "New Super SLR" pulls a bit more cable (around 15% more, I think) which in theory means 15% less braking power for the same hand force. Shimano's compatibility tables show dotted line compatibility between "New Super SLR" levers and "Super SLR" calipers, which they say means "Braking power is slightly less than standard combination."

I've mixed them and IMO it works OK. I like the feel better when they're matched, but mixing is OK. I suspect you'll get used to it.

That explains it. Thanks! It kind of feels like when I used some canti levers with v-brakes on an old mountain bike only not as extreme.

If you now also have different/new brake pads that might account for much or all of the difference. Pads can have a profound effect on brake performance.