Yup.
I would wait.
They're exhaust bolts. They've been heated every time the engine ran. You'll never get penetrating oil all the way down to the threads, at least not until you've gotten the bolt heads turned far enough to leave a gap at the manifold, or broken the head off. I have no faith in "working them back and forth", but I guess other folks do.
"I" would grab the longest-handle 1/2" ratchet I owned, (about 2 feet long) and SLOWLY/CAREFULLY/GRADUALLY apply reverse torque
using a six-point swivel socket and supporting the ratchet head with my other hand, while using extremely harsh language. The long handle allows for the
control of power not just "more leverage", while the swivel socket prevents side-force on the bolts.
Maybe you get lucky, and all the bolts come out. It's possible. And if they break...they break. Remove or break as many bolts as needed to get the manifold off, then weld nuts onto the broken shanks and try again, or pop the cylinder head off as needed.
It'll be about the same deal at the Y-pipe flange, except you have the option of using penetrating oil and/or an oxy-fuelled torch. (Oxy-Acetylene, Oxy-Propane, Oxy-MAP-Pro.) If you aren't using extra oxygen with the fuel, it won't be hot enough.) My machinist buddy brags up the success he's had removing seized fasteners by "marinading" them in penetrating oil, sometimes over a weekend, sometimes for an entire week. Good luck.
All I ever get out of penetrating oil is a spot on the pavement where it drips off. You can try to remove the nuts, but the studs will likely break and then you either buy a new manifold or you spend time with the torch getting the broken stud(s) out of the manifold.
When the Y-pipe goes back on, use BRASS NUTS so they don't corrode to the studs. Some folks suggest stainless nuts, I've never used stainless.
Auto parts stores sell stud-and-brass-nut kits for exactly this purpose. Thread pitch/size varies, be sure to buy the right parts to fit your manifold.
For example:
www.napaonline.com/en/p/NOE6001930
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