At full bump and articulation my tires go so high that they'd crash through the stock fenders and hood. To prevent this from happening I chose Genright aluminum fenders. The aluminum offers welcome weight savings over steel and are lighter than factory.
I figured out a way to make a perfect cut on the hood with no guesswork.
First mount the both fenders in their final positions. Take your time and do this right. Since my 37" tires will still be pushing into the flare by about 1/2" at full articulation I mounted the tub side on the higher end of the highline mark of the tub to get the most out of them and then aligned the front to the grill. Additionally, tighten down the center grill body mount and grill support rods. It's disappointing that Genright doesn't make the radius perfect where it meets the grill — I could slide a small stack of business cards between them.
Now put tape on the grill and tub and make a mark where the top of the fender is (needs to be the highest point). Take a laser level and line it up so that it draws a line between both of those markings and it should put the laser line straight across the top of the fender. This laser line will mark where you need to cut the hood.
Unless you have 2 lasers you'll have to repeat the steps above for the other side after cutting the first.
Remove both fenders leaving the grill supports tight and close the hood. There's 2 rubber bumpers on the bottom side of the hood that need to be in contact with the grill. Remove the spring from the hood and/or have a friend hold the hood down firmly. Check the gap between the hood and the grill is even. With the friend still holding down the hood put tape along the side of the hood where you will be cutting and trace the laser line onto the tape.
Cut off the bottom of the hood. I used a cut off wheel on an angle grinder which created some heat so I had to move quickly so the heat wouldn't mess up the paint. I found that making the cut in a single pass made the smoothest line but don't worry at this step if you mess up, it's the "practice" cut.
Repeat the cut on the other side and mount both fenders back up to their correct alignment. Both of mine aren't exactly the same cuts, even if you look at a clean TJ the hoods don't sit perfectly symmetrical on them either.
If the hood rubs the fender when closed use a flap disc to remove just enough to slide a sheet of paper between the fenders and hood. Remember, this is practice so don't worry if you cut a little too much off.
Replace the tape with fresh and run a marker with a 1/2" body along the top of the fenders so you have a straight line on the hood 1/4" off the fender. This is the final cut line.
After making the final cut I removed the burr on the bottom edge of the hood by hand so that I wouldn't remove too much material. If any of the paint is damaged sand that off with finer sandpaper. I got some music playing and enjoyed cleaning it up for the next few hours.
When the bottom of the hood is removed the spot welds holding the front hood brace onto the hood are also removed and allow the rubber bumpers to move in. To firm it up I used 3M Rigid Piller foam. It's pricey stuff and requires a special "double barrel caulk gun" to use but I haven't seen anything else like it for cheaper. I already had the tool from working with body panel adhesive and seam sealer. The foam is runny when it first comes out so seal the gap with duct tape and leave only a small hole for the tip of the mixing tool end to fit in. Also put down something over your engine and fenders in case it leaks out.
I got a little excited on the first side and used too much. You only need somewhere between 1/8 and 1/4 of the tube per side to just get enough in that it expands past the indentation of the support (see arrow in picture below).
Let the foam cure over night with pressure removed from the crossmember.
The next part is the retaining latches, the factory OEM latches with the rubber is best since it allows the hood to move with the body just like it was designed to from the factory.
The bottom piece has a bump that recesses into the factory fender this needs to be cut out so it sits flush to the fender.
OEM fender mounting holes:
Figure out where you want the latch along the hood, measure carefully, and drill the 3 holes into the fender.
Fasten the lower latch piece to the fender. This will allow you to position the top onto the hood. For right now loosely place the oval hood to fender spacer to gap the hood. There should be a slight gap between the 2 hard pieces of the latch assembly with the hood fully closed. Align the pieces, mark and drill the hood. And bolt everything together and repeat for the other side.
Test your latches to make sure everything is working properly. The latches should be just as easy to use as from the factory.
Lastly, place the hood to fender spacer, mark and drill for it. This will hold the hood to the 1/4" gap. Because I couldn't fit mine in the same direction as factory I rotated it perpendicular to the hood.
I used touch up paint to prevent rust.