Is my duct transition choking the airflow after a furnace swap?

The whistle and the weak bedrooms are almost certainly the same problem, and it's the transition. When air has to squeeze down through a smaller opening and then hit a sharp angle, it speeds up and you get that whistling, and everything downstream of the restriction suffers. The far bedrooms losing air fits that exactly. It's not your imagination. A gradual rebuild is the right call when you get a Saturday. You don't need to copy the old sweeping curve perfectly, you just need the sides to flare out slowly instead of stepping out all at once. Make the transition longer than you think it needs to be, and if the height difference is what's forcing the sharp angle, consider dropping the furnace plenum or building a taller box so the air has room to spread before it turns. Even a plain rectangular transition with gently sloped sides will quiet that whistle down alot. The old guys bent those big sweeping boots because they work, but a decent sloped one gets you 90 percent of the way there. Before you rebuild anything, check the cheap stuff too. A whistle that starts the second the blower kicks on can also come from a filter slot that isn't sealed, a loose blower door, or a return grille somewhere rattling. Put your hand near the joints on the return side when it's running and you'll ussually find the leak in about a minute. On the barometric damper, don't just leave it alone. A new furnace fires differently than the old one, so the draft the damper was weighted for may not match anymore. If it swings freely and isn't stuck or rusted open, you're probly fine for now, but the right move is to have it set during the tune-up you're allready planning with the oil tech. Since you're adjusting the air to hit those combustion numbers anyway, the overfire draft should be checked at the same time, because the damper weight affects those readings. It's a five minute adjustment for someone with a draft gauge and it makes your other numbers mean more. One more thing since you're doing ductwork on the next pass, seal the return joints with mastic or foil tape, not the cloth stuff. Return side leaks pull basement air into the system, and that's exactly where you don't want air coming from.

Did a similar swap at my own place a couple years back and chased a whistle for a week before I found it was the filter slot cover, not my ductwork. Worth peeling that back before you cut metal. Also, the new blower might just be moving more air than mom's old one ever did. Mine shipped on a higher speed setting and dropping it one notch calmed everthing down and actually balanced the rooms out. Might buy you some comfort untill your free Saturday rolls around.

Agree with checking the blower speed first, that fixed it for me too. Swapped out my mom's old clunker last fall and the bedrooms went cold overnight. Turned out the installer had it on the highest tap out of the box. Dropped it one speed and the whole house evened out in ten minutes, no sheet metal needed. Your manual should show which wires are on which tap if you want to peek before cutting anything. Might save you that Saturday for the rebuild instead.

Before you cut metal, wiggle the old trunk downstream of your transition. Mine did the same thing after a swap, whistling and all, and it turned out one of those old snap-lock seams had let go from me bumping the duct all weekend. Twenty seconds with a screwdriver to reseat it and half the problem was gone. Also try taping a couple of cardboard ramps inside the sharp part of your transition, just as a test. If the whistle calms down, you know the rebuild is worth the Saturday.

Update: checked the blower like a couple of you suggested and sure enough mine was on the top speed tap from the factory. Dropped it one and the far bedrooms evened out right away. Whistle is still there though, so I guess the transition is still pinching things. Question on the barometric damper though, does that need any tweaking after a swap or should I just mess with it?