’91 Honda Wagon Engine Swap the Problem?

I think this is the correct category for this question? I bought my civic three years ago as a cheap AtoB. The automatic tranny was rough back then, and the thing still goes! It’s true what they say about this generation of Honda. The thing is, if I really want it to continue to go, I think I need to solve the tranny issue which I believe is truly an engine SWAP issue.

The original engine was swapped out for a D16Y7 engine. This engine is not popular, but I think it’s pretty cool for a fuel econo build because it’s a 1.6L aluminum engine which means light weight.

However, the tranny is stock, the ECU is stock OBD0, and there have been no adjustments made to the fuel injection, which is stock.

From my research I understand that transmissions before 1996 where not hydraulic, and apparently some sort of adapter is required for older model trans to 1996 and up engines?
I have also been told that the hydraulics are how the transmission works – and nothing to do with the connection to the engine or how the engine drives the transmission… I have no idea.

The OBD0 has no way to read the sensors from an OBD2 engine. So I am not sure what the oxygen sensor is connected to…

And since the OBD0 cannot read the sensors from the newer engine, I do not think the correct fuel/air ratio is happening at the injectors especially because the stock engine was 1.5L…

I want to keep this engine. Do I fix this transmission, and get a new ECU? (I am thinking aftermarket instead of making everything work for an OBD1). I WANT to convert to manual, many people say its not worth the effort. If I have to get a new tranny anyway, what, all I would have to do is get the pedal assembly, angle grind a clutch pedal whole in the firewall install the assembly, and install the clutch cable and new center console, right? I mean, yeah it’s work, but is it really THAT complicated?

WWYD?