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To the best of my knowledge, B and D series use the same engine side mount, and most transmissions have a different side mount (the mount that holds the transmission to the car), because the posts on the transmission that the mount bolts to are different. However, B and D series are popular enough that you can probably find a mount for the transmission and chassis combination you want.
The tallest transmission that bolts to your engine is the B18B Integra LS/GS transmission. The most efficient engine that will bolt into your chassis is probably the D15Z1 from the 92-95 VX. The wiring from a 96-00 engine (such as the 96-00 HX's D16Y5) is probably easier because the wiring will be more compatible. All D series transmissions bolt up to all D series engines so you could use whatever one you wanted. If you set your mind to it, you could make any D or B series engine work with any D or B series transmission, in your car. Some will simply be easier / less involved.
Ultimately though, it's probably more cost effective to swap cars than engines. VX's are relatively rare because people like to buy them to put different engines in, but HX's aren't that hard to find. My absolute favorite 90's Civic is the 92-95 VX, and I was lucky enough to get one for free from a forum member.
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