Q: Can i put a transmission from a 99 honda civic into a 98 honda accord?

The 1999 Civic transmission has a Tag ID (stamped on the transmission) of B4RA. The Tag ID for the transmission used on the 1998 Accord with the V-6 is either B7XA or B7XA-1. Inasmuch as these transmissions are electronically controlled, if the Tag ID of what you are installing is not absolutely identical to the original Tag ID, the transmission with not work with your existing computer and wiring harness. The difference in the Tag ID also makes it likely that there are differences in the gearing and calibration of the valve body. Even a "single" difference in the transmission could render it effectively incompatible but in this instance there are probably a dozen or more design/calibration changes.

Rebuilding your existing transmission ensures compatibility and rebuilding transmissions is frankly easy. Although used transmissions are NOT recommended for installation, if you are looking for a used transmission for rebuilding purposes, simply go to Car-Part.com and you will find an exact match for your car (there are many listed). Transmission swaps on modern computer controlled vehicles must be EXACT matches because if you attempt to use a transmission that is not cataloged as a direct cross reference, you will find that the engine and transmission computers are not interchangeable. Consequently, even if you can get a "different" transmission to physically fit, it will not operate properly and the PCM will spit out error codes. If you are interested in a transmission replacement, YourMechanic professionals in certain locales can assist with that. Please simply inquire based on your locale. If you have further questions or concerns, do not hesitate to re-contact YourMechanic.