Ok I have several options for gearboxes & diff to use none of wich will be a direct fit and will require modification in one way or another...

With this in mind I may aswell go for the one which will give me the best final drive ratio.

The indy will have 250-300HP with plenty of torque & a 5 speed box.....

Ideally what speed should I be looking at achieving for each gear?
i.e
1st 35mph
2nd 60mph etc

If 0-60 is your target then the top speed in 2nd wants to be 62+mph I'd guess. With that level of power and torque on offer you could run pretty high gearing.

My 3.62 with a type 9 does 39mph in first, thats 7200rpm and 140mph at 7200 in 4th.

Switching to 2nd lights the back end up and I have to fight the snaking that results...

With the amount of BHP and Ft/Lbs you will have available i would seriouslly look at a close ratio gear set.
The gear set available from Quaffe or BGH would be much better than even the T5 box
I would sugest the 2.5 1st gear and 1.6 second, this will give depending on diff 45 in first and 65/70 2nd 90+ 3rd.
I find a 3.3 1st to low, a big gap to the 1.8 2nd.