Obviously modifications are best determined by your driving style, needs, and preferences, but if it was mine (and since I own a beautiful original-owner Reflex Silver '03 Golf 5M with "tasteful and preventative maintenance") mods:
Preventative:
1) Maintenance: As said, make sure all maint is up to date, including some items that could use a refresh at 20 years/200k miles, such as suspension, all rubber bits, and some of the "additional" items often done at TB change. LRR tires will increase FE (Nokians for the win). This list could go on and on, which is why it's first. Even on a well-maintained car, time will take a toll on everything from the rubber antenna mast and base, to wiring in the engine bay and hatch, to plastics and hoses and tubing. Have you done a refresh of all the vacuum lines? Cleaned behind the wheel well liners? 200,000 mile diesel purge? Greased / lubed all the hinges and contact points, inspected the CV boots, replaced the GPs with a touch of anti-seize on the new ones, and installed a new tire on the spare wheel?
2) Skid plate: IMO, a Panzer or equivalent skid plate is high on the preventative list for most MkIV owners, and if it saves you a single time, it's worth it.
3) VCDS: Add a Ross Tech cable to your tool box, if you've not done so already.
Tasteful:
1) If I lived in Florida, I would tint the windows. Tint comes in a full range of VLT, including almost clear, so there's no need to think of it as an aesthetic mod, but obviously a darker tint will provide additional privacy, and keep prying eyes away from the interior contents. High quality tint, regardless of darkness, will lower interior temps, decrease AC use, and subsequently (in the heat) you'll see a FE bump. Even a 50% tint (what she has on her Mk7) is only slightly noticeable from the inside, yet makes the interior a significantly nicer place to be on a warm/hot day, and a cop would never be more inclined to pull you over (not that it happens much in FL, where limo tint seems common). You may also find that a slightly darker shade really shows off the Reflex Silver (mine are 40%, which is a world away from limo 5%, and it makes the silver pop).
2) OE VW alloy wheels. Losing weight at the corners will increase FE and you'll notice a bit more eagerness in stop and go driving. The heavier steel wheels can be replaced with lightweight VW Avus (or other style) to keep things stock (since I loathe aftermarket additions), and you may be surprised at how they refresh the appearance after 20 years. I have found the VW steel wheels seem to dent rather easily, and hubcaps crack, get lost, and to my eye, say "GL" model.
3) Lighting: I'm a big fan of lighting mods, and the NA Jetta/JW headlights are terrible. It's late in the game to easily get new OE Jetta lamps, but I'd find Hella or Valeo units, maybe E-Codes, with integrated driving lamps, add a Euroswitch, and wire them up. As long as you're replacing the switch, find one with rear fog lamp position, and convert your tail lamp to mimic the proper European style. A rear fog light has saved me several times in heavy rain/fog/inclement weather. I'd also add Hella DEs to the lower grills, but as said, I enjoy lighting mods.
4) I'd swap the OE 4 spoke vinyl steering wheel for a MFSW (or 3 spoke GTI wheel is you prefer). I never like the OE plastic wheel, and the steering wheel and stick shift is what hands grip most often while driving. I'd also swap those seats for the black cloth GLI/GTI high bolster sport equivalents, or add lumbar, but that's a body shape/seat preference.
Other thoughts:
1) A roof rack typically isn't necessary (especially for a wagon) unless you have a moving/long trip planned that requires additional space. Even an unloaded roof rack can seriously lower your FE, so leave it off unless needed.
2) Engine: If your engine is running well, I wouldn't change a thing unless it was part of maintenance. The nozzles may be tired after 200k miles, so one size up would bump usable power and increase FE, and make sense as part of routine maintenance. IMO, the EGR delete hasn't been an issue since ULSD, (I believe it both for a minute and for the last decade, at least for my car) and keeping the emissions system intact helps when laws, locations, or situations change. IMO, the VNT15 is perfect for daily driving, and proven both reliable and helpful for engine longevity. A mild tune, especially in conjunction with new nozzles, might help with FE and power, but wouldn't at the top of my list. As far as I have seen, excessive engine mods tend not to correlate well with longevity.
3) Transmission/clutch: I wouldn't change the clutch until it's needed (or required due to the slippery slope of various other engine mods). A different 5th gear only helps if you are on the highway most of the time, and you may be annoyed by the gap between 4th and 5th. A 6 speed swap is a costly but attractive alternative, and lower RPM may increase your FE at highway speeds, as well as lower engine drone.
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