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I swapped a 2.5 out of second gen Mazda3 into my 06 Mazda3 sedan & went ahead a put a 6speed from a second gen 2.5 as well to replace my 5speed, my bottom gears aren’t shifting,only goes into reverse 1st, 3rd & 5th. Any advice? I used the cables from a second gen & used the shifter box from a speed 3
 

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So I just got done doing the swap and I ran into the same issue you did.

What's happening is the shifter rod on the speed3 assembly sits farther back on the assembly than the regular mazda 3. Because of that, you reach the maximum travel distance of the shifter before the transmission is able to engage the gears.

My solution was using the regular 5speed shifter assembly and making a custom reverse lockout as to not go into reverse by accident and everything works great.

If anyone has any more questions about this swap feel free to ask.
 

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So I just got doing the swap and I ran into the same issue you did.

What's happening is the shifter rod on the speed3 assembly sits farther back on the assembly than the regular mazda 3. Because of that, you reach the maximum travel distance of the shifter before the transmission is able to engage the gears.

My solution was using the regular 5speed shifter assembly and making a custom reverse lockout as to not go into reverse by accident and everything works great.

If anyone has any more questions about this swap feel free to ask.
So I have a 2005 Mazda 3 manual transmission and I want to put a 6 speed manual transmission transmission in and keep the 2.3l can it be done
 

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So I have a 2005 Mazda 3 manual transmission and I want to put a 6 speed manual transmission transmission in and keep the 2.3l can it be done
Yes. You need to find the 6-speed from a 2nd Gen mazda 3. NOT from a mazdaspeed 3, just to be clear. The 2nd Gen 6-speed is a direct fit to the 2.3. the only difference is the threads on the transmission mount bracket, so you'll need to transfer the one from your 5-speed to the 6-speed. Also, since the first gen didn't have a 6-speed model, there is no shifter assembly available that has a reverse lockout. You'll need to get used to not accidentally going into reverse, but it took me only about 3 days to get the hang of it.

Side note: I suggest you take the opportunity to do a balance shaft delete, change the rear main seal, and replace any clutch related components while your transmission is out if you had plans of doing so. Your life will be so much easier. If you don't want to buy the baffle for the balance shaft delete, you can replace the oil pan with the one from a 2.0L. It's also a direct fit and has a baffle plate in it already since the 2.0L doesn't have a balance shaft.
 

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Ok thanks I have a speed 3 shifter and gen 2 cables and currently only have 1st through 4th no 5th or 6th so I'm going to swap over to the factory cables and shifter
Don’t use the speed3 shifter either, it won’t work. You need to use the original 5 speed shifter. They bolt to the same spot, but if you put them beside each other you’ll see that the speed3 shifter sits farther back in the assembly. If you use the speed3 shifter you won’t be able to shift into 2nd, 4th and 6th.
 
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