My goals are similar to yours. Here is what I have done or will be doing shortly:
1. Fix the rust on exterior (small amount) and under the carpets (bigger amount). Had to remove the fenders to fix the leaks causing the interior rust.
2. Repaint
3. New OME suspension
4. New Procar Elite lumbar support front seats
5. Replace all the weatherstripping around the doors and windows (including windshield and cargo area windows) with OEM, add WagonGear weatherstripping, and sound deaden with RAAMMat
6. Replace rear view mirror with a new auto dimming mirror with compass and outside temp (Gentex)
7. Fix all the oil leaks and any other mechanical issues that have been ignored like steering/front end parts and brakes. Since my rig is an fj62 with a 3FE engine, I also proactively replaced parts that get old and have been known to cause problems like O2 sensors, fuel pressure regulator and fuel pressure dampener. Also replaced vacuum hoses, radiator hoses, etc. My 3FE sounds like a sewing machine--very smooth with just the right amount of click.
8. Upgrade headlights (Daniel Stern), LED dash lights, and new horns (no more beep beep for me)
9. I plan on driving it for another 100K/10years, so my cost (including purchase and restoration) when spread out over the 10 years is less than $100 per month.