It entirely depends on usage.
With regards to brakes, a decent two pot 7.5" or 8.4" setup will suffice for general road/fast road use. Those alloy four pot vented kits are pointless unless you race your car and are regularly using your brakes heavily. Then again, some people will happily waste money on shiny things, it's up to you.
Engine, again, it entirely depends on what you want. We can't really give you ay more information unless you tell us what you want. If it was me, I would be looking at building a reliable unit producing a sensible amount of power with lots of low down torque for road use. It's all very well having a hot cam, but if its power range is between 3000 and 8000 RPM, you're buggered if you want it for road use.
Gearbox. If it were me, In would spend some money rebuilding the gearbox and fitting an X pin diff, just for peace of mind. If it's not for race use, don't bother with straight cut gears/drops as they are just noisy and in road conditions, you won't notice any benefits. You may want to change your final drive ratio. You can choose a long or a short FDR depending on whether you want top speed and economy or acceleration. My personal favourite for road use is 3.44 as a compromise. Although, engine speeds of 4200 RPM on the motorway is unacceptable for some.