Having owned a 99.5, they're a special beast. No immo = good. Hot start glitch in the ECU = bad (solved with tune). Wobbly MK3 shifter mechanism = bad (solved with upgrade to later style shifter upgrade).
Other than that and a few odd wiring harness differences they're all ALH all the time.
Manual? If so, I'd grab it if it's clean and rust-free. May need a few things, but nothing on these cars is that difficult. The shifter isn't as precise as a later MKIV, but if the parts are in good shape it's fine. If you weren't going from one to the other (like I do) I'm not sure you'd notice particularly. Besides, the OP had a MKIII, so he doesn't know different.
Greens: don't buy it, it is grossly overpriced. Get them down to $1500 and then only if it is rust-free like IBW said. Besides, being a loyal follower on this site, you already know the tons of stuff you're going to have to do to it as soon as you get it home anyway, right? There, now you know why it is overpriced.