Sounds like he's already got them to the same ratio. If I'm reading this right,
Started with: 3.55 front 3.07 rear (D30 front from someone else's aborted swap)
Now has: 3.55 front 3.55 rear ( replaced rear w/ a D35 from JY)
Don't worry about the speedo until you get your lift & tires dialed in, just know that it's a little off and drive accordingly. Heck, in most lifted Xjs you can't break the speed limit by much anyway ;-).
You should decide about what gearing based on how you plan to use it. Crawling? You will want deeper gears. 4.10s at least, 4.56s if you think you will ever go larger on the tires. Daily driver and weekend dirt road wheeling? You will probably be fine for a while with the 3.55s, and save your money for skids, armor, etc.
There are as many opinions about lifts as there are people with lifts I think. Just read a lot on here and decide for yourself. People will tell you to go big right away but that can cause more hassle than it's worth, what with having to get a SYE and stuff.