I would keep the auto as a daily driver and plan todo no mods to it. The A4LD trans was junk in those cars and thats why ford detuned the car limiting boost to 10 psi.
One good thing abotu the stock motor is if you loose a cam belt the head is noninterfence meaning the pistons will never touch the valves no matter what.
under the lower intake are a couple hoses that I would replace. they can be a pain but it is just a good idea.
I would also check the turbo for shaft play, if it rubs the compressor housing expect turbo failure soon. If the car sat for two years theres a good chance the turbo seals are dried up and you might end up replacing it anyway.
To try and keep that trans life high install an aftermarket fluid cooler for it. it makes a world of difference.
TC dashes are known to crack, so good lucking finding one that isnt. You can buy some things online to clean the cracks or you can buy a dash pad/cover for it.
Change plugs,wires,cap,rotor and use all motorcraft parts.
Go to www.rockauto.com they have everything you need
parts store brand equipment always seems to crap out but if you have to use parts store use NAPA b/c quality is way better. Same with filters use motorcraft FL-300 for oil or the 1068 napa.
88 thunderbird TC 2.3L
Gillis at 18 psi, walbro fuel pump, Kirban afpr, 3.73 8.8" rear, rebuilt head, Ranger roller, .48/.60 T3 with clipped wheel, ported elbow, 3 in exhuast, FMIC
66 mustang V8 swap baby
68 Fairlane 289 w/ auto
rusting away motor is going in the mustang