Good to hear another abandoned project is getting put back on the road. After 20 years, I'm sure you have your work cut out for you, but it should be a fun project.
Besides my B (which was abandoned in a garage after a minor traffic accident by a colleague's son for 2 years before I bought it), I'm now working on another "barn find" - an '88 RX7 convertible left top-down and uncovered for 5 years in an open garage full of feral cats. No rodent damage, but it smells like a litter box and the seats have suffered for it.
Back to your car. First some clarifications. You say it has a pair of DCOEs. The B head, unless a cross-flow coversion, has only 2 siamesed intake ports, each feeding 2 cylinders. The Weber DCOE conversions I have seen utilize a single 2-throat side-draft carb. Twin carbs of this type would require a strange manifold with twin y-pipes, each to a single port in the head.
If the DCOE is in good shape (I expect it will need a cleaning and minor rebuild at least), I would stay with it.
If you do choose to go original, there's a market to sell the Weber kit and regain some of the replacement costs.
I would also suggest looking at using the HS6 conversion rather than finding and rebuilding an original HIF4 set of SUs. Though the HIFs are more modern and easily maintained, they are not available new. If you insist on original (which you've already said this will be a driver when done), Joe Curto in Queens, NY can supply you a quality rebuilt set, but you'll be on your own for linkages, manifolds, spacers and heat shield, all readily available used, but the HS6 kit comes with most of this included and offer better performance at what would be similar costs.
When you say the manifold "fits hard" to the exhaust, I think you mean the the manifolds butt again each other with no clearance at the studs (side-to-side), right? Unless it prevents the manifold from seating, it should not be a major problem, but that's actually an easy fix. You can grind the edge to open the gap and improve the clearance, which is usually more easily accomplished on the intake manifold as it is aluminum.
Another fix would be to replace the exhaust manifold with a header set. Those would be of stainless or mild steel and should be fairly accurate to the OEM piece, but more flexible than the cast iron in the event of being tight. Again, if the clearance is tight, it would be easier to modify the intake slightly, filing or grinding the clearance needed.
I hope that helps you. Please write and ask any questions as well as updates as you progress.
Safety Fast!
Art