just wondering whether or not the axels are different in the automatic and five speed? i have a 99 ex and it is automatic, and a buddy of mine gave me his manual tranny for free. arent friends great!!!

 

The drive axles for a 99 EX Automatic are the same for a 99 EX Manual transmission, (at least thats what Honda says) however you were not clear as to what the manual transmission is out of so hopefully this answers your question.

 

Nice swap.....goin from Auto to Manual.......Congrats!