on the subject of tuning IRTBs, biggest issue is that you'll need to tune on TPS, as you wont be able to get a solid MAP signal for them...this is no biggy....your tuner should be able to deal with this. You'd also want to make sure that the throttlestops are all set the same so you get an equal amount of air into each cylinder under all conditions.
on the subject of the bonnet, have you considered a removable scoop, that you can mount a panel filter in for road driving - and remove completely for bare naked throttles on the track? just an idea