I rec'd finding a good BMW oriented Indie in Philly area; a quick GOOG perusal shows several of them. Have them give your X a thorough look and estimate on what it would take to get it pass PA inspection. My guess is that $8Gs from the dealer is 2-3X what an Indie will charge to get you past inspection, maybe less.
Once inspected and legit, you can then decide if you want to dig into suspension, cooling sys replacement, etc.
5 spds are not common, though not a 'collectible' imo. If you do off it, it will be worth a lot more to someone, if it has passed PA insp. and/or could pass NJ inspec. Without that sticker it screams 'big dough to fix'. A 5 spd would be interesting to the right buyer, if you do decide to sell it, though the 6 spd is even more rare and desirable, imo.
As you say, it starts, runs, gets you around and you like it; get the sumbitch repaired to pass inspection, and then take you time on deciding what you should do, imo.
'01 X5 3.0 Sport, 5 Spd Manual, etc.
'02 VetteVert 6 Spd, Z51 susp.
'10 Hyundai Tucson for the CEO, & 3 Assorted M'Cycles.
BMW CCA mem. Tarheel Chapter
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