It could be a lot of things, are you 100% sure it's coming from the tranny? I'd try to check that first because it could be a wheel bearing or even something rubbing.
If you are, it's most likely a bearing. Usually when you replace a clutch you replace the throwout and pilot bearings and you'll be able to check those when it's apart. If it's inside the tranny... I'd look for a replacement but if you can't find one, cracking the cases open isn't super difficult but it's up there.
Any 89-91 Civic/CRX d-series tranny will work, but they have different gear ratios depending on the model. The Si is the shortest geared in the US (there is a ZC transmission overseas that was shorter), DX was 2nd (actually has same gearing as Si, just different final drive), and the HF was by far the longest. There was also a 4 speed that came in the base Civic's and a 5+low tranny that came in the RT Civic Wagons.
88 Civic/CRX transmissions have a different spline count on the input shaft so avoid those.
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