Not much to gain on these N/A engines I'm afraid. I dropped a K&N filter in which was nice and cheap + gives you that "I've done my first mod" feeling. Makes no real world difference though. (If you do this check it after a day or two. Because the filter is vertical heat from the engine can make a drop or two of oil collect in the bottom of the housing)
I haven't really done much else apart from the odd bulb/LED and a period head unit. Still fancy some spacers though, I do think that would improve its looks no end. Not a mod but Waxoyl might be an idea.
Re your first point, at 16 years old and 195k I'm tempted to say stop doing that then!
Secondly, my IS300 is very sensitive when it comes to wheel balancing. Get that checked first. I also have a slight clonk nsf that no one seems to be able to track down so I've stopped worrying about it.