Stem change and proper angle...
 

The reach on my Roubaix is too long. I'm gonna change out my 110mm / 12° stem for a shorter one, maybe a 90mm or even a 75mm. If I go with the 90, should I consider a 17° angle to compensate for the slight bar height loss? Or, if I go even shorter with a 70mm stem, would a 24° angle be the way to go?

go where a bike-shop has those choices and try them.

You can compare the current setup with either of your options with this online calculator:
Stem Comparison Tool | yojimg.net
Play with the angles of the new stem, as well as with the thickness of the necessary shims.

Why do you think your stem is too long? Fitter?

Just feel too stretched out. By all indications my frame size of 61cm is correct, but my reach just feels too long. And I probably have my saddle too far forward because of this, and that's causing me some knee pain. I'm 6'3" but my height is all in my legs. Short torso, but arms are maybe a bit longer than average.

Didn't have hardly any problems with my hybrid Giant Roam, but this Specialized Roubaix has been most difficult to get dialed in.

Doubt that knee pain is from saddle position. I understand that's the conventional wisdom, but there's no evidence for it. Reductio ad absurdem, recumbent riders do just fine vis a vis knee pain. However knee pain can certainly result from incorrect saddle height. Usually a too high saddle makes pain in the back of the knee, too low in the front of the knee.

With your saddle where you like it, while watching in a mirror or having someone photograph, put your pedals horizontal, your back straight, your hands on the hoods, and your forearms horizontal. The standard road position would have your elbows in front of your knees and your upper arms making a 90° angle with your torso.

Many riders have accustomed themselves to a cramped fit from a previous bike which was too small. Very common.

I tend to agree with the above. First things I ask myself if I start feeling knee pain is if I've been riding a low cadence in too high a gear t0o often. Next is have I been hydrating adequately.

It might be a controversial subject, but what size cranks are you riding? Some people think that crank length should be proportional to height or leg length. I disagree.

A longer crank will work your knees through a longer range of motion. More chance of pain IMO.

Fit is very personal and everyone has a different idea on what is ideal. Might need to try a few stems to find out what you like. Just go to ebay and pick up a few to try. They aren't that expensive and once you find what you like then maybe get a better quality one if you like. Actually the one I got for like $10 is pretty good and might just keep it...

The stem comparison tool says that the 24° 75mm stem would keep the same elevation as your current one.

I would agree that the top tube length combined with the steep seat tube angle is probably giving you more reach than you want or need for a leggy guy. But you might want to try getting fitted since you have knee and reach issues.

Since you're tall I would put the bars as low as possible. Get the 17 and flip it -17 and slam it :-). The lower you go the shorter the stem needs to be. Where is your knee pain, front or back? Here's how you adjust fit to end pain: https://i2.wp.com/www.monaxle.com/wp...whyyouhurt.jpg

Geometrically, this is absolutely not true.