The battery light came on yesterday on the way home from work.I checked the voltage at the battery and it was only 11.65 volts and dropped to 11.58 slowly as it ran.Checked all battery cable connections and checked voltage at the alternator.It was less than half a volt.I removed the positive battery cable and the engine stalled.I went for a short drive to see if the lights would dim.They did, and when the battery got low the transmission started to slip.When I turned off the headlights it re-engaged and I drove the last block home.I replaced the alternator today and am getting 14.36 volts at the battery.The battery light is off now and the lights are bright, but the speedometer does not work, and the light for the cruise control doesn't come on. I am wondering now if the speedometer works off the alternator,the transmission slipping while driving with the battery low caused damage to a sensor, or I possibly damaged a wire while changing the alternator.Ive checked the cruise control fuse and for any visible wiring damage.My search brought up many with alternator and speedometer for 1997 Honda Civic in the same answer.

. Check all under dash and under hood fuses with a test light or multimeter:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-3.html#post252145

Since you have a multimeter, with which you tested your charging system, I would not have removed the positive battery cable, while the engine is running--it's asking for trouble with the ECM, alternator, and sensors.

. Clear any codes with a code reader.

. Remove and clean the connector to the Variable Speed Sensor (VSS). Check VSS wiring.

. Replace VSS, if problem persists.

As TxGreaseMonkey stated above, check the alternator fuse. I had a similar problem in my 1997 civic, and replacing the blown 7.5A alternator fuse was all that was required to get the speedometer working again (after replacing the alternator).

So you yanked a battery cable while the engine was running? Then it's very possible you fried the instrument cluster. That's the worst possible way to test an alternator. See the article below.

How to test an alternator (http://www.ricksfreeautorepairadvice.com/repair-topics/alternator-generator/alternator-testing)