On a budget I know SSBrakes makes a bolt on disk kit that will work on the drum spindles and match up pretty well with the rear drums.
Drop the mounting location on the front arms 3/4". The old Shelby mod really helps handling on a stock set up.
Those little 289s sound pretty good and run decent for a daily driver. A nice recurve on a Duraspark distributor with an MSD6AL box will spark it up easy in the mornings and clean up the idle characteristics. For the distributor you can contact Tim O'Connor.
www.428cobrajetcars.com
You can buy an MSD for more $$ but no reason, same reluctor wheel trigger as the Ford. MSD just copied or licensed it.
Is it a 4bbl? The 4100 Autolites on those are as dependable as a carb gets. same goes for the 2bbl version but that small 4bbl is worth a few bucks to the Mustang guys. Also you can support a stout 289 with the 4100.
A set of 351 hipo exhaust manifolds work pretty well in there and with a good set of turbo mufflers will give it a good sound.
For a transmission if you want an OD use an AOD out of a Fox Mustang. No computer control needed and it will pretty much bolt up. A stock take out from pick a part should get the job done behind the little 289. You may even be able to use the C4 driveshaft. Really though the C4 will last forever and is a good three speed auto so unless you are hot rodding the car I'd just leave it.