OP, been there. It was a headache. Try this:
Passenger side manifold to midpipe connection uses a crush seal. Ford OEM or Fel-Pro are the only two brands I've had luck with.
There is a lip on the gasket. That lip goes up, towards the manifold. You'll see what I mean when you get in there.
To drop the H pipe from BBK, it's going to be one solid unit. This means you'll need to disconnect the driver side and loosen up the connections to the cat back, or even remove it for clearance, to do this. My best advice is put a jack under the center of the H pipe before unbolting anything. This will ease with reinstallation of the H pipe when it comes to height. A common problem is people install these midpipes and don't account for ground clearance and they complain they sit too low. If you but a jack under it before you unbolt anything, once the new gasket is in you will know what height to bolt everything back to because the jack retained the height for you.
The driver side is going to be a ball and socket connection. Torque the hell out of it. I don't know if BBK came with a sleeve inside but this doubles as a reducer and spacer. The stock studs on the driver side has a collar. The reducer in the mid pipe not only takes the stock outlet of 2.25" and allow it to mate to the 2.5" pipe but it acts like a spacer so the driver side can tighten up correctly. You'll see what I mean about the collar on the stock studs on the manifold when you get in there. For me personally, I couldn't get a tight connection so I had to replace the OEM studs with aftermarket without the collar. You don't have a problem with the driver side so this shouldn't be an issue but just incase.
On the passenger side. Install the crush gasket with the lip towards the manifold. Put the H pipe into place and tighten. I always tightened to 34 FT/LBs. This is because I've read overtightening can cause the gasket to deform and not seal. At the time a member told me to go with 34FT/LB on the passenger side and I was good to go after that. You'll need extensions and a swivel joint to get the passenger side studs - especially the furthest stud closest to the body.
I've had a Jegs O/R H pipe, Summit O/R H pipe, BBK O/R X pipe , UPR O/R X pipe and MAC O/R H pipe. Don't ask - 10 years of ownership and I wanted the perfect exhaust note. I found H pipes that are solid generally fit like crap and hated it and I just generally hated them all honestly EXCEPT for MAC. MAC was a 3 piece design that utilized studs at the joints and made for amazing fitment and sealing. FYI if you get fed up with the BBK H.
If you really want to go all out, like I did, and just get tired of messing with it all... I just went long tubes. Some say it isn't worth it, and it isn't performance wise, but the sound and ease of working on it now is bar none. It'll set you back in the $1k range between the headers (I went BBK Ceramic), new midpipe you'll need and labor (because they SUCK to install yourself. I gladly paid the $350) but to me it was worth it. Everyone's opinion will be different.
It's all based on your mechanical ability, budget, and willingness to figure this quirk out. I personally hated that stock design from Ford and after market mid pipes really gave me a headache except for the MAC piece.
Good luck