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I'm kidding about the trans being out. My problem is I don't know how long it will last, of course none of us do. That's almost 5 grand then plus the turbo, man of man! A couple months ago I sent in a oil sample that Shaeffers give out free from the trans and it came back good. My problem is trusting it when I had two of them crap out on me. Do you think it can be done OK with it in? O rings, 1" housing and then the D66, getting fairly good at takeing out the turbo. When I had the last one rebuilt I keep saying put the very best parts in, if you can't get them I'll order them from racer x or what ever. I think they did a good job! The racer x valve body really helps with the normal slipping changing gears.
Neals brother Jason did his with the trans in he saids it wasn't to bad. He messed with it a couple hours a day and took him 4-5 days. It can be done in a weekend.
Yeah, the uppipes actually come in from the top side, so you can do it with the trans in the truck. I took mine out thinking it had to be taken out, but they had to go in from the top.
I'd say it could be done in a weekend if you could work on it constantly the whole weekend. Mine took much longer than neccessary because of clearance issues. Different uppipes and the physical size of my turbo is much bigger than the S300 is. The S300 fits without any clearancing.