i have never seen a gearbox with same size gears running between the layshaft and input shaft. looks normal to me.
top speed 4th gear with 4.3 axle ratio at 7,500 rpm is 189.5 kph or 118.4 mph. which would be about right for a race track.
i think your getting confused over normal reduction in gear ratios for 1st, 2nd and 3rd and overdrive for 5th. 4th being a direct drive.
the S2000 gearbox does not have a direct drive in any of the 6 gears. they are either underdrive or overdrive. but for some reason Honda don't take into account the reduction gears when quoting the gear ratios. i suspect the gear ratios that Toyota give are the actual input to output ratios. i only mentioned reduction gears as a possible answer to the op's apparent short top speed.
so with a one to one gearbox ratio and an axle ratio of 3.5 the top speed in 4th would be 232kph or 145 mph which would make cruising better but probably not pull top revs.
quick summary all worked out for 4th gear 7,500rpm top speed with 205/60x13 tyres
4.3 = 189kph = 118mph
3.9 = 208kph = 130mph
3.7 = 220kph = 137.5mph
3.5 = 232kph = 145mph
top speed 4th gear with 4.3 axle ratio at 7,500 rpm is 189.5 kph or 118.4 mph. which would be about right for a race track.
i think your getting confused over normal reduction in gear ratios for 1st, 2nd and 3rd and overdrive for 5th. 4th being a direct drive.
the S2000 gearbox does not have a direct drive in any of the 6 gears. they are either underdrive or overdrive. but for some reason Honda don't take into account the reduction gears when quoting the gear ratios. i suspect the gear ratios that Toyota give are the actual input to output ratios. i only mentioned reduction gears as a possible answer to the op's apparent short top speed.
so with a one to one gearbox ratio and an axle ratio of 3.5 the top speed in 4th would be 232kph or 145 mph which would make cruising better but probably not pull top revs.
quick summary all worked out for 4th gear 7,500rpm top speed with 205/60x13 tyres
4.3 = 189kph = 118mph
3.9 = 208kph = 130mph
3.7 = 220kph = 137.5mph
3.5 = 232kph = 145mph