If your Jeep runs fine with the 3.07's, I would stick with them until you do your lift and bigger tires. The difference between 3.07's and 3.55's isn't much; however, lots of people who have 3.55's stock, stick with them with 31's. Even though it isn't the perfect tire/gear match, it still works pretty well, and is certainly better than your 3.07's. There are a lot of variables here such as how much you drive it, your terrain (in the mountains vs. flat land) and how soon you are going to upgrade. Last year I replaced my boss' 3.07's in his YJ with 3.55's. He swears that the difference is super-huge. I drove it and I think he should have gone with 3.73's or even 4.10's. Either way, he had been driving it on 3.07's and 31's for years without any problems. It just comes down to whether or not you want to spend a day swapping axles.
You didn't ask for it, but I'll offer some extra advice: I install a lot of gears/lockers for people and the one piece of advice I always give is this: Once you pick your tire and gear size, go one gear size shorter (numerically higher). Everyone I have done gears for always has the same concern: "I don't want my engine over-revving at speed" and they always have the same response after the install, "I wish I would have gone one size up." The misconception is that your mileage will suffer from the shorter gears, which is true at highway speeds if you go with crazy short gears. Where the true problem is, is when you're driving in town or try to drive up a grade (where most of us wheel). There, your engine has to work harder to take off from a stop (similar to a 10-speed bike in the wrong gear) and your gas mileage will REALLY suffer. I am not exempt from finding this out the hard/expensive way. I run 35's and I went with 4:56's and it is a dog off the line and in the hills and it is nowhere near revving high at freeway speed (which is usually 80 MPH for me). I have a set of 4.88's in the garage waiting to be installed. If they made 5.13's for the D-30, I would be putting them in instead. Once you do your lift and tires, gears are one of the best ways you can get back or even improve your vehicle's power.
Good luck!