I hadn't seen this solution to routing the vacuum lines when swapping the older log-style intake for the 99+ version so I thought I'd give it a shot today during my manifold swap.
I pulled all the vacuum ports out of the new intake and tapped the holes for 1/4" NPT fittings. The outer two side ports got 90 degree 1/4" inverted flare fittings. I bent up some 1/4" steel tube connecting the new fittings to the locations of the two missing vacuum ports on the top of the intake. I know I could just buy longer vacuum hose but I like being able to order the stock plastic lines and have them fit without issues.
Here's the intake almost fully installed on the Jeep. It's a little blurry but it was 25 degrees out and my phone wasn't cooperating. I know the throttle body spacer doesn't add much if anything but I made it myself and I like it.
And just because I'm proud of it here's a shot of the intake ports showing the work I did cutting out the excess metal from the center four injector bosses. They are all the same size now.
So far I'm liking the new manifold but I've only driven it a couple miles.