Yes the Bronco pan will work I am told (an old Hotrod trick though I have never used one) and you can mate it to the stock trans. This has been done zillions of times and it works just fine. before good automatics or four speeds came around in the sixties this was the ONLY option, bolt a late model OHV motor into an early Ford, that was it, pickup a fifties hot rod mag and this is ALL you will see. Look for adapters for that trans and just about every engine under the sun has been bolted to those stock Ford trannies, I have had many Buick nailhead both early and late adapters over the years. And as far as disc brakes and the like, it really depends on your expectations and how you are going to drive it. I have driven MANY miles on the old stock drums and to me unless you are doing some serious canyon carving or high speed driving the drums are PLENTY good.
I would bolt that 289 in and have fun!