I can take on just about any project related to a jeep BUT gears. I just dont have the tools to do it correctly.
So I farm out all gear changes to a local drivetrain repair place. I take the axle out and pressure clean it real good. remove the guts of the diff and clean in there too. I pop all the seals and get them a clean housing. They charge me 80-150 to set up a new set of gears most times. I also tell them I am in no hurry so they can work on it when they can.
I found my 8.8 with 4.10's which was a relief. This was after I geared my D35 and D30 to 4.10's myself. I should have never put the money into the D35 but you live and learn.
As far as gears go they are more tedious and require some tools but I think a seasoned backyard mechanic can do it with enough research and preparation. Hell, I was able to to do it so I'm sure most can
You can talk to whomever you're going to have put the gears in for you about buying them assuming its a shop. Either way, going from 3.07-4.10 will require a new carrier and I would suggest purchasing one that isn't openable open differential. There are lots of options out there on the market including the selectables or even a Detroit Autolocker which both would fare well with the CAD still in place.
Just think long and hard about your next two moves before you make your current move. Building a jeep is a lot more like chess than Legos.
Depending on what axles go for in your area, (around here i can buy any front axle for $67 and any rear axle for $32 from a local u-pull it yard) it would most likely be cheaper and easier to find a D30 from a 4 cylinder jeep and swap it in then buying new gears and paying someone to do it for you. And while having the axle out of a jeep you can clean it up, paint it and replace whatever you feel is necassary before installing it.
Then you can probably sell your original axle and break even or maybe even make a buck or two.