Just pulled the manual transmission on my '01 civic with 260K miles to replace the rear main seal and clutch. This is probably the first time it has been pulled. I'm hoping it will also be the last. Is it worth doing any work to the transmission while it is accessible? ie Are there seals or bearings on the transmission itself that tend to go at a certain mileage point? If not, I'd rather not dig into it if I don't have to. But if so, it probably makes sense to bite the bullet and spend the extra time and money for parts and labor while I'm here. I've had no issues except maybe twice a year pops out of second into neutral.

 

Since you already have it out, open it up and clean the magnet then reseal it.

Also, check your synchros while you have it open. Shift all the gears with your hand and see how smooth it goes into each gear. Look closer at your second gear and the slider going from second gear to third gear to see if you can find anything that causes it to pop outta gear. Compare all the synchros to see if they are evenly worn.