Gents, long time lurker here. I finally decided to register so I could add to this discussion. I own a '98 SE 5-speed with 145k miles. I'd like to comment on a few topics here.
If shopping for a 4th gen Maxima with a manual transmission, your only options will be in the GXE or SE trims. GLE was not available with a five-speed. As well, I doubt that GXE was available with leather interior, so that might narrow things down to SE trims only. The SE included slightly stiffer spring rates, fatter sway bar, nicer 16" alloy rims and some aesthetic changes (i.e. chrome delete, body-color trim, white-face gauges, et al.) For the range of model years, Nissan made a mid-cycle update in 1997. Agreed with above, they were mostly cosmetic upgrades. Generally the '97, '98 & '99 cars more desirable, with a couple of caveats for the ‘99’s.
There aren't too many instances of systemic failure points. There seems to have been some occasional transmission issues although I'd say the odds are no better or worse than other 15-year-old cars with MT’s. A notable failure of the '99 SE-L, however, is its coil packs. They eat them like no other 4th gen model, even after replacement, and they aren't cheap. For that reason alone I would avoid '99s unless you're tolerant of occasionally being stranded. Finally, '99 is also when the immobilizer key debuted.
My Max is almost totally stock with the exception of a few mods (CAI, front strut tower brace, Addco rear sway bar.) The MEVI intake upgrade was a popular one and does net approx. 30 HP for not too much effort. Y-pipe replacement is another although there were quality control issues with some of the vendors. Replacement shocks / struts / springs were always hot topics, lots of discussions about Tokico Blues vs KYB GR-2’s vs KYB AGX’s. All variety of lowering springs are available, some pretty drastic. There are also turbo & supercharger kits for those with money to burn.
Generally the car has held up well but is starting to show its age. Interior has held up really well, very few squeaks & rattles. Exterior is in decline, with rust starting behind both rear wheels and at the spoiler mounts on the rear deck. Mechanically I have made a lot of repairs... both front lower control arms / ball joints (which can't be pressed in for replacements), wheel bearings, sway bar bushings & end links, three of four tie-rod ends, front & rear calipers (on my third set of rears now), o2 sensors, knock sensor, exhaust & evap system. Amazingly I'm still on stock suspension although it's getting a bit bouncy/rough. Stock clutch as well with no signs of slipping yet.
I was semi-active on www.maxima.org for a long time, the forums are an excellent resource and one reason why I bought the car.
If I was in the market now for a Maxima, I would definitely look for an ’02 or ’03 with the 6-speed. A close second would be an ‘03+ Altima with the 3.5L and manual transmission, there seem to be more of them available on Autotrader / elsewhere. Good luck!