Absolutely. In my case, I don't have the ability/time to shorten an axle, so a TJ44 was the best option (aftermarket axles being another, but quite pricey). If you have the skills and spare time to build your own axle, go for it hands down.
This is my dilemma. Really want to try 5.89s, going in with the assumption that I'll need to get manual hubs, but slightly worried about the rear having vibes too. It's my understanding that the LJ's longer driveshaft doesn't help with those vibes either..
If you don't have high lift, and driveshaft angles are precisely correct, and the driveshaft is not too heavy and properly balanced, you should not have vibes at any speeds. The only factor that you don't really control is the driveshaft balance - I think that they are balanced up to 3000RPM, and with 42RLE and deep gears will get into 4000+RPM area easily.