In the GameSpeeds file are a series of entries defining the number of months that pass on each turn. Each game speed has 7-8 entries in this table, and they're processed sequentially; so, on Standard it might say that the first 65 turns pass at 480 months (40 years) per turn, then the next 75 pass at 240 months per turn, and so on. If you add up the seven entries for Standard, you get 500 turns; that's the maximum number of turns you can play before the game ends in a Time victory.
That 500 value is also used to determine what year you start in when you select a different era in the advanced setup menu; in the Eras table, each Era has a value <StartPercent> that specifies what turn number that era starts on if you're doing a late-era start. So if Industrial starts have StartPercent=50, then it'll start you on turn 250, whatever year that corresponds to from the GameSpeeds table. (Again, this assumes Standard speed, which caps at 500 turns; Quick caps at 350, so that same StartPercent=50 would start you on turn 175.)
So in your scenario you changed the start year from -4000 to +2000, but you didn't adjust any of the rest, so it's still going to start you at 40 years per turn for the first hundred or so turns, then drop to 20 years per turn, and so on. If you want a different progression, then you just need to adjust all 29 of the entries in the gamespeeds-month correlation table. (Or since you're doing a scenario, delete all 29 and then add four of your own, one per game speed.)
Alternatively, you could leave the gamespeed progressions unchanged and simply try to start your scenario on turn 400 or something. That'd put you in the standard game's time progression, but it'd cap your scenario at 100 turns.