I had GarageFive do the 5speed swap on my 97 Prelude a very long time ago.
If I remember correctly, I paid about 1300 for parts, some new and some used. All from someone parting out their damaged Prelude from vancouverpreludeclub.com (way before the original site shut down)
I think it was 1500 for labour at GarageFive? I can't remember of the top of my head, I'll have to find the invoice and double check but roughly 3K for the entire conversion.
Here is all of the information for the swap:
VancouverPreludeClub.net ? View topic - Automatic to manual transmission swap
RomPirate’s 5spd Swap Resource Thread - Honda Prelude Forum : Honda Prelude Forums
The official auto to manual ECU conversion thread - Honda-Tech
I think you are better off to sell your auto prelude and buy 5speed prelude. It seems a lot easier to me.