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You may need to go to a big rig shop, and either purchase a short section of 4" exhaust pipe, or if the filter needs to be turned, a 45* or 22* section of pipe will make it lay straight.
It might help to remove the first section of intake pipe and rotate it and the filter together to find the best place. If you can post a picture of what you have might help.
I went to NAPA...they had a 12 foot piece of 4 inch exhaust pipe. They cut me a 3 inch section and a 4 inch section. I used the 4 inch section....cost me about $10 for all of it.
4" long piece of 4" pipe and your in buisness. BTW I just got my cover from Pete in the mail today and the picture didn't do it justice... if it wern't dark and *31 F outside I'd probably put it on now... then again I may still
The early 99s have a much shorted intake hose -- not at all like the one in the pic above. It ends about where that one crosses the I/C tube. He will need a length of tubing like Kris described.