I've just got around to fettling the gear ratios, and stumbled upon another issue I'd seen mentioned elsewhere, but never fully understood.
The ratios available to place in the gearbox itself actually depend on the "maximum speed" setting. That is, setting the maximum speed to the maximum (261 mph, or equivalent) gives overall taller ratios for every gear, decreasing both the maximum and minimum in the selectable range. E.g. first gear can be between about 3.5 and 5 with max speed set to 261 mph, but it can only be between 5.5 and 7.5 with max speed set to 112 mph.
This means that the ratios used in the standard box cannot be selected in the fully custom, since the available range is not wide enough for all gears to be correct. Setting the "maximum speed" value to the minimum that allows the top speed (i.e. ratio in top gear) to be accurate results in the minimum ratios available for first, second, third and fourth being too high, so that the ratios are too short in those gears. Adjust the maximum speed setting to the maximum that just gives the correct first gear ratio at its minimum range and the opposite is true: fourth, fifth and sixth are now all too tall.
Also, the actual range of ratios available per gear varies with maximum speed - at 261 mph, the lower limit for first gear is ~ 70% of the upper limit, at 112 mph it's ~ 75%. The relative range available in each gear is different, too: 2nd gear's lower limit is ~ 80 % of the upper limit at 112 mph.
Oddly, the final drive is unaffected, and its extremes can produce some very silly ratios indeed, so "preventing silly ratios" is not a defence of the system as-is. However, the final dirve setting will affect the range of ratios available after changing the maximum speed setting.
The maths is clearly messed up, and I don't really know what they were trying to achieve here! What was wrong with the gear selection interface in GT1? It even had quick-scrolling using R1 and R2. The mind boggles, it really does.
Until they fix this issue, as well as the engine inertia and clutch physics, this car will continue to be horrendous without resorting to mild tuning.
EDIT: I found a compromise in gear ratios that gives something close to the ones I posted before, assuming the stock ratios are all missing a 3/2 step down. I tried to get as close as possible within the limitations of the interface by exploiting the final drive setting bug I mentioned above. First I set the final drive to 3.800 and then reduced the maximum speed to 112 (minimum) and selected the ratios in the "fixed" column below. Then I set the final drive to 2.780 to get the correct ratios overall (except sixth).
Gear....Real......Fixed.....Relative (%)
1st.....4.154.....4.884.....100.0
2nd.....3.000.....3.620.....97.5
3rd.....2.367.....2.812.....99.0
4th.....2.100.....2.470.....100.0
5th.....1.875.....2.197.....100.4
6th.....1.760.....1.873.....110.5
Final...3.270.....2.780......--
Note that only sixth gear is grossly incorrect here, and is too tall by about 10 percent, which serves to increase its theoretical top speed. Be aware that these ratios have only been tested with the car otherwise unmodified, but it is a vast improvement over stock settings and retains the overall character much better than the close ratio options (except for sixth gear, of course).