DON"T LISTEN TO 45 CAL....The 03 SO (Standard Output) and older CTD came with the 47re Transmission.
The 03 and 04 HO (High Output) 5.9L cummins Turbo Diesel came with the 48re transmission. They are just as capable as the 04.5 CTD's except they have 20 HP less at the crank and 55lb/ft of torque less. Which a power chip can change very easily!
****EDIT for 45 Cal***
***45 Cal....all your knowledge on the CTD is on your 04.5. Dude....I still have my bill of sale and WOW.... you would be amazed 48re 4 speed automatic on my 04 High Output 5.9L CTD. You should actually do some research on CTD's before you comment on anything but your 04.5 CTD. You will actually find out that 03 and 04 High Output 5.9L CTD's with the 4 speed auto came with 48re Transmission.
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The 04 HO Cummins Turbo Diesel came with a 3.5 inch Turbo to muffler exhaust and 4 inch muffler to tail. The nice thing about the 03 and 04 HO Cummins compared to the 04.5 and newer was no Litter box (Catalytic converter).
The 04.5 and newer come with 4 inch turbo back exhaust system but with a litter box.
I have a 04 CTD with the HO and I placed on the Edge Juice with Attitude, AFE stage 2 CAI, and a diamond eye free flow exhaust. I kept the 3.5 inch pipe to the bend and added 4 inche pipe beyond and located the Diamond eye muffler where the stock was sitting. I have had no issues with power and EGT's.
The 4 inch turbo back exhaust is the way most guys are going to keep the back pressure up for towing or lauching as a larger 5 inch you will lose alot of low end grunt/torque but gain power in the higher speeds.