Bought an 06 civic DX and knew it had transmission problems. So I budgeted to buy another transmission.

Now upon further research I'm baffled. Some information I am reading says just change the fluid, some says the 5th gear needs to be replaced that it is a common problem, some suggests clutch.

What the car does is have a very hard time engaging in 1st when taking off. So you have to rev high. It makes a rattly sound when idling kind of like the sound of a loose heat sheild rattling on exhaust. And when driving in 5th the shifter will pop out of place and go into neutral.

Any suggestions? Also is the 5th gear a guaranteed problem eventually? Ie. I don't want to just pull another used tranny to end up having a known issue such as the 5th gear give out. If this is a known issue is there an upgraded gear set I can buy to replace it with now? If so where can I buy it as I've had no luck.

Or is there another manual transmission I can use that will bolt up to R18 motor?

This is an R18 motor with a 5-speed.

 

What type of oil are you using now? Try some amsoil mtf and see what happens. My 06 si had the 3 gear issue where it was hard to shift into it. I replaced the fluid with OEM honda mtf and still did it. Then I switch to amsoil and the problem went away. It might just be a temporary fix but it doesnt hurt to try.
The ratting sound could be either your throw out bearing or your input shaft bearing.
If you barely depress the clutch while idling and the sound goes away its the throw out bearing most likely.
My 2014 accord has a bearing noise and I narrowed it down to the input shaft bearing. I will replace the fluid soon with amsoil mtf and see if it holds up for a while until I have the funds to get another transmission.
Input shaft bearing also make noise when you accelerate on lower gears (2-3 preferred) and let off the throttle abruptly, you will hear a whine as the car slows down and then go away when you accelerate again.

 

I have no idea what is in it as I just bought it the other day lol. Have decided to flush and fill with fresh mtf. I have the funds to replace trans if need be though. Would just rather spend it elsewhere lol

 

Also what viscosity ams oil did you use? I see 2 one is a 5W and one is a 75W

 

Popping out of top gear normally begins from the lack of fluid... which overheats the internal parts. The first gear issue sounds like a worn out clutch, so check that if/when you remove the transmission. Drain the trans fluid first... and catch it in something so you can quantify how much was in the trans to begin with. If there was approximately two quarts inside, this is likely not your problem at this time although this may have been a problem before you purchased it. If a quart or less comes out... pull the transmission and find a quality replacement.

 

It's really not as hard as you think to touch up a 5 speed tranny versus an automatic, which is way too much for the novice backyard mechanic

the sound you hear at idle is always the input shaft bearing, and that's not that hard to replace

there are howto's on youtube for replacing the input shafting bearing on a honda d series transmission and it's likely not that much different on this one and there is this one for replacing the synchros and stuff

 

I understand how to replace the parts I just cannot find them for sale here in Ontario. The only place I have yet to contact is Honda themselves. I have found your typical wear parts such as clutch, flywheel, hydraulics but no one seems to sell the gears, synchros etc for this particular transmission.

 

5w30