Check out this site http://www.tnvjc.org/
Look or ask for Bill (admin) aka Jeepsonly. He's the one that did the writeup and should be able to answer your question.
FWIW I think that once the pipe has been routed around the oil pan it will line up with the stock exhaust.
95 YJ 4.0 w/36'' and some other stuff
I'm in the middle of this install. I ordered a '99 manifold (Same part # for the '94), a '99 Magnaflow down pipe & Catalytic converter, and an OEM muffler. I went with the Magnaflow because it is mandrel bent and full stainless steel. Here is a link:
Install of the manifold went really smoothly, bolted it all up no problem (Thanks to the shop who installed the previous one using anti-seize on the bolts). Went to put on the down pipe and it doesn't fit. Its bent too far such that it won't line up to the manifold without hitting the oil pain. Not to mention the flange bolt holes are too far apart to line up to the studs and it won't reach the studs anyway.
I assume the problems are stemming from the down pipe not being manufactured properly, and not a generic TJ > YJ problem? Anyone who has done this swap care to add their experience?
ETA: Looking at this stock photo on Autozone's website, it looks like the Walker down pipe has a much less shallow bend directly off the manifold than the Magnaflow one I received.
And here's the Magnaflow piece: Notice the might tighter bend.
White '94 YJ Sport Black '98 ZJ Laredo - 45x60 Surco Rack - 2" Budget Boost, Addco Front Swaybar
I used the walker downpipe on my YJ, I bolted right up without issue. I did have to use a few reducers to mate up with the flange that mates to the cat. The pipe clamps leak a little, I would weld the reducers up if I did it over again.