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i just recently converted my 99 EX from an auto to manual. Everything is running fine,but i have yet to switch the ECU to the 5-speed. I plan on doing it sometime in the near future, i was just wondering how much they usually cost and if i didn't switch it, what problems would i be running into? everything is running alright with the auto ECU....
 

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You might be better off just leaving the auto in there, otherwise you are in for some work! The idle air control valve is different between manual and automatic. Yours is on the throttle body and uses 3 wires, the manual is located on the intake manifold and uses 2 wires. If you switch ecus you will need to do one of the following:
1) Swap your manifold for a manual version w/throttle body and IACV
2) Get the 2-wire IACV, take your manifold off, drill & tap it for the new IACV.
3) Live with the issues caused by having no idle air valve.

If you're not having problems right now, there's no reason to change the ecu.
 
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