Phil, no hijacking at all, it's all about sharing information and inspiration....
What I do is compare the two tubs and find a common point away from the area that is to be changed. For the defrost section, that is the empty holes on either side of the YJs duct indents in the dash center section. (E and F top pic and B and C bottom pic) Measure to the edges of the tub and such to confirm these holes are in the SAME spots. Using a speed square, draw through the center of each hole. (the straight edge is offset when drawing so the thickness of the line is the center) I use a fine tip Sharpie marker. For the long front most line, the thickness of the line is drawn such that the inner edge of the line matches the outer edge of the holes. (top pic B) Do this on the CJ part first. The center section that is left (where A is in top pick) is left where no material is lost in the cut. Transfer the same lines to the YJ tub EXACTLY with many measurements to confirm.
Next thing is to check for straightness in the overall parts. Was the cowl/defrost area bowed down or twisted from a wreck, etc. Squat down and run your eye down the length of each part to check for warpage, etc. When you cut out the donor CJ parts from the bad tub, try to cut larger than needed and not distort the metal that will be used. That's why the defrost section is rough cut below where the cowl seal would go.
When cutting the lines,I use a fiber disc on a dremel tool and score a nice groove FIRST for two reasons, it allows to blade to track in it and stay straight....and the dust and debris doesn't cover up the groove as easy as a pen line gets covered.
So your question, what side to cut..IF IF IF the lines are correct, cut the CJ part first and cut through the lines.(the blade removes the line and is in line with the line) You did it right if you can stand the CJ section with the long front cut on end and the oval holes are the same size and straight.
The YJ tub gets cut on the inside of the line, (D and C side). The line is left and the cut runs right along side it touching it the whole way.
How to cut.... Make a starter slit with the dremel about 1 to 1.5" long. Use a fine tooth blade on a reciprocation saw (sawzall). A wider and short blade works best as it stays stiff and straight. Don't cut 90 degrees to the work as most other stuff is cut. This will pull up and push down on the metal stretching it. Instead, lean the saw back and cut shallow and along the line. It goes slower but cuts longer and straighter in the metal and allows you to view the cut better as it goes. Don't jam the blade. Also use the fastest speed. Final fitment is done with trail fitting and a light touch with a flapper disk on a angle grinder.....light touch only where needed. Welding magnets help hold it flush for the spot welds.
I'll have to just shoot video when I do the next YJ tub.....I have a few to do still.
I used a 18 Volt Dewalt reciprocating saw for the cowl and a Dewalt 18volt jigsaw on the gas filler hole. For the oval holes behind the tailgate hinges, I used a hole saw and a jigsaw and all were cleaned up with a corded angle grinder using a course flapper disk.
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