I am currently in the middle of a 3.4L swap in my 94 4Runner. The headers are installed and the engine is in the bay....but the passenger side header is hitting the frame. Has anyone else run into this? Can the header be altered in any? What gives???

 

Mine didnt hit the frame but it is a tight fit. The header collector can be cut shorter to allow for a fitting that will clear the frame.
You might need to persuade your brake line to move a little and wrap your fuel line with insulation.
some pics.

 

The frame huh, got any pics? Are you using 3VZ-E or 5VZ-FE engine mounts? Do you have a body lift, I don't see why it would matter but the Downey catalog says the 3.4 headers "do not fit vehicles with a body lift"

 

Not sure why it would matter if there is a body lift. But as of right now I have a Roger Brown 1.5" body lift that is not yet installed. This is needed to clear the 3.4L in my 94. I am using the 3VZ engine mounts.

I like your idea about insulating the fuel line but I removed mine and re-bent the line to stay completely clear of the header.

I have heard of others actually cutting and rebending the header pipes to clear. Hopefully I will not have to do this.

 

Hi,
The third gens that this header was made for had some problems with the rag joint hitting the EGR port on the header. I've called and asked Downy and that was the answer I recieved about the lift question.
Now on my 2nd gen with the 3.4 I had to have the EGR port on the header removed to clear the steering shaft. The rag joint isnt close to the header EGR port its the steering shaft thats a close fit. Like you I also used the 3VZE engine mounts.

The pass side collector is a very close fit between the frame and the clutch slave cylinder. I didnt have to trim my collector but you might have to so you can clear the frame. The fuel line in this pic will be reworked to allow some more clearance but it hasnt been a problem so far (winter temps).