I would actually leave the bottom spring in. If the tranny shift isnt firm enough for you(it will be pretty quick, and quite firm with the spring), then you can drop it out. But many have felt the shifts were TOO firm with no bottom 1-2 spring.
DEFINATELY do NOT leave the top 1-2 spring out. Just replace it with the correct one listed in the JMOD tech article.
Definately remove the 2-3 spring. it will give you the best 2-3 shift you could ever imagine.
I went with w Hayden 26k cooler. It cost $74. including shipping. I dont know about Mustangs, but with my Mark VIII, I also had to roder proper fittings for the cooler lines in the heat exchnager(radiator). Go to Bulk-part.com for those
If you leave the bottom spring out, you will have not only a nice, quick shift, but it will be very firm as well. My 94 mark VIII 1-2 shift was too firm for my tastes. I was chasning the rear end all over the place everytime it shifted into second, if the ground was damp at all. I went back and re-installed my lower 1-2 spring, and it was pure perfection.
Best of luck, and enjoy the new "toy". It will feel like a whole new car.