2000 accord 2.3l l4 f23a engine. I used manual transmission from a 98 accord. Tried to use ECU but car wouldn't start. So I tricked gear position sensor and used automatic ECU. Great, she starts and runs just fine. Got her out of the garage and the driver side cv axle ripped out 8 feet from the street!!!! Dang! Ok so here's my problem. I ordered a half shaft for my year model accord and I recieved it, cool it has two make ends trans side has 27 splines, cv axle side has 27 splines. I ordered cv axle for my year model and it has two male ends half shaft side has 27 splines, to wheel hub has 28 splines just like wheel hub. Cool but I can't put two male ends together. So I take the cv axle back and get one with a female end 27 spline. Cool it works, no! It rips out its not long enough. The accord version has two male ends, he prelude version has one male one female but too short. The only half shaft I find has two male ends... What in the **** do I do here? I know plenty of people have done this swap. Everyone else said my year accord cv axle would work but it has to make ends. Am I missing something? I'm a chic that just wants her car back. Please help/ just shy of customizing my cv axle I don't know what to do.

 

Are you using an Accord mid/jackshaft or a Prelude one?

When converting from AT to MT always use the axles for the car(Accord). Prelude axles are similar but not correct for use in an Accord.

 

I'm not positive, but if your running a 98 trans, I'm assuming it's an F22 unit, it will still take a Accord 5 Speed/manual trans axle.
All of the axles including intermediate need to be changed to manual trans. Accord units. They may look the same laying on the ground but 10mm will result in a c-clip not engaging or holding. If you've done the 98 accord manual drive shafts and have an issue with spline count at the hub side then it has to be swapped as well. Be sure your motor is sitting level and drive shafts aren't at different angles. I did a 96 auto EX Accord wagon to H22 5 speed swap and had similar issues with shaft popping out and motor mounting woes. There was a difference in DX, LX, & EX auto and manual mounts, mount posts, and frame mounts, the differences between 94,95 & 96,97 models as well. It is a head scratching deal with multiple ways to compound problem as well as solve. Don't let it get you down because it's worth it in the end. Like the saying goes, " if it was EZ everyone would do it." Once you get it sorted out its something trick that you've built. There's no better feeling than accomplishing a goal and contiueing to enjoy it whenever you want.
Also be careful where or who your sourcing your parts from, you sound like a knowledgable guy so check Rock Auto and use there site to really see what's available and what will work together, it helped me a lot.
GLWB