I have a 90 Mustang 5.0 with the EFI, and jusy installed a NV3550,
the 3550 is the best 5 speed for a daily driver, its very nice, I havent run mine on the interstate yet with the NV so I cant comment on the MPG, but in town didnt change, but its a lot more fun driving the 3550 than a T-18.
the cheapest way to go is just get a whole donor car, like a Thunderbird or mustang or crown vic and yank the engine and seats and sell whatever sheetmetal parts are left over, and scrap the rest.
The 88-91 EEC4 is very easy to work on, once you understand how it works
this book explaines it in a very easy to understand manner.
http://www.amazon.com/exec/obidos/tg/detail/-/0837603021/102-6675526-0543369?v=glance
the EEC4 is very versatile, once I had my upper intake manifold off, along with the throttle body, and the mass air and throttle position sensor, and one fuel rai, 4 injectors removed, and I hit the key and it CRANKED and ran!
on any other type of system if you unplug just one sensor, say the mass air sensor, the engine will not run at all,
I use the 4 core Wild Horses rad, and have NO cooling issues ever.
Ive had probs with the fuel overheating, but thats due to install errors on my part, ie: using rubber fuel lines instead of steel.
I am planning on adding AC, but mine never goes over 170 on the gauge, unless the water gets more than half empty.
One thing to consider also is a good alarm and a GPS/cell phone tracking system, and an appraisal and check with your ins co about a stated value coverage, cause if you do all this stuff to it, and do a shiny paint job, it will be attractive to thieves, and your ins co wont pay you anything. maybe $800.
Power steering and disc brakes are another thing to have for a daily driver,
if you have the $$$ Id recommend doing all the mods at once, its much easier to swap engines and transmissions at the same time,