There is a difference when comparing 3 spd trans to 2 spd trans.... there is less drag with a 2pd vs 3spd, which gets more power free, i forget the formula for each gear but it's a fairly substantial difference.
The 904 didn't have the low 1st gear we all use in the 727, the 999 did, and the 904 and 998 didn't get the 2.7 1st until after 1980, so his trans if it is a 04 isn't the one to want to dick around with for the BB, which then it'll need an adapter anyway.
The reason that you went faster if you used the 999 gearing over the 727 was that the 999 had the 2.7 1st and 1.5 2nd and the 727 had the 2.4 and 1.4
So if you have the factory 727 and the same car has everything you do but it has the 999, you lose. If you have the 727 with the 2.7 1st and the same car has the 999 it becomes closer but it'll be close.
Going from the factory 727 gear to the 999 gear, you'll get a few tenths, going from the 2.7 1st 727 to the 999 you'll get close to a tenth probably, if he has a stl shaft you get the AL shaft and then you're faster till he gets the AL shaft....