Welcome to WF, glad to have you here!
Ok, your '04 LJ has the 42RLE automatic transmission which is actually a 4-speed. Its 4th gear is Overdrive.
And while 4.56 and 4.88 is an appropriate ratio for 35" tires with other transmissions including the 5-speed manual (4.88) and older 3-speed automatic (4.56), your particular transmission has such a high Overdrive ratio (which produces low highway rpms) that you need a minimum of 4.88. Even 4.88 is not quite enough gear for 35" tires, 5.13 or even 5.38 is a much better ratio as it will lug a bit with 4.88 on the highway with engine rpms being a bit too low.
Unfortunately, your front Dana 30 can only go as low as 4.88 so that is the gear you should go with. Don't even think about 4.56, you'd hate it.
After my last TJ was stolen, I bought a replacement with the same exact 42RLE transmission, 35" tires, and 4.88 gearing. I wish it had 5.38 and even the previous owner, a friend of mine, admitted he screwed up by not having gone to 5.38. Mine has a Dana 44 up front so it could have been regeared to 5.38 which would have been better.
So the bottom line is go with 4.88. While performance won't be as good as it would be with 5.13 or 5.38, it will be adequate. Not so with 4.56.
Enjoy the forum!