Rep Power: 0

Here lately my 99 LX has been making a thunking noise shifting from 1st to 2nd, it's almost like a hard shift, only I can only really hear it and not feel it. it almost sounds like hitting small pothole or something

gearbox fluid is fine, not burnt, not dark black, but not bright pink either. I plan on doing a home flush to it at some point soon...

any ideas? How prone to failure are these gearboxes?

 
Rep Power: 210

Do and ATF drain and fill. Google 3x3 atf drain and fill if you want to go that route.
Locate the shift soelnoids on top of the transmission housing, clean the solenoid gasket screen. You can test them as well: http://troubleshootmyvehicle.com/hon...lenoid-tests-1

Could also be an inner CV axle issue?

 
Rep Power: 0

Any recommendations on cleaning the solenoids? What should I use?

 
Rep Power: 210

Brake cleaner spray or throttle body spray will work.

 
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Also, What would cause it to kind of jerk when it goes into torque converter lock-up? It seems like anytime it goes into that, I can feel it jerk into lock-up....

 
Rep Power: 518

Those cars were kinda like that. Probably normal.

Later cars (7th gens) got a bit smoother about engaging the TCC.

 
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so, it's nothing to worry about? Is there anything I can clean or adjust to make it a little less jerky?

 
Rep Power: 210

Follow Dong's advice in reply #3. Use Lubegard red additive to the drain & fill.

 
Rep Power: 518

IF it is normal, then it's normal and nothing to worry about.
But if it is not normal for that type of car/engine/transmission, you can worry.
Duh.


So figure out if it's normal and typical. Or not.
If you can find someone with an identical car that has no complaints about their transmission, drive it (or have them take you for a ride) so you can experience it and compare with how yours drives.

If it's normal, then no.
Routine fluid service with proper Honda spec fluid (DW-1) is always encouraged.

Those cars always shifted rather firmly. You KNOW it shifted a gear when it does.
Got failing engine or trans mounts?

 
Rep Power: 0

will do.

And I am not sure if they are failing or not, The car does seem to vibrate alot and sometimes it feels like the engine is bolted directly to the chassis rather than through mounts. How do I check if they are bad? Is it the same any other car? (Putting in gear, foot firmly on brake - giving it gas and seeing if the engine moves alot more than normal?)

 
Rep Power: 518

That's one of the first things to try.

Visually inspecting the rubber portions of the mounts is another, and seeing if any have collapsed or been mis-assembled--that mount on the nose of the engine....the hardware may have been missed during a timing belt or saimilar service?