The '99 XJ intake was still the old log style. The XJ only got the curved runner intake in '00-'01.
While it's true that the mods I suggested will only yield small gains, the cost is also small. A performance cam is really a waste of time unless you port the head while it's off and if you're going to go strip down 2/3 of the engine to do a cam swap, you might as well go all the way and build a 4.6 stroker 'cause you'd probably need to refresh the bottom end of a 12 year old engine anyway.
Once you've done that, all those other little mods I mentioned earlier will complement the stroker build so they're still worth doing.