I just got done doing the swap on my mustang. Here are my recommendations
1)stock pushrods will work fine
2)change the cam. Even a stock HO cam is better than the exploder cam
3)Get a MAM and/or dyno tune. Mine runs funny because the C&L 73mm doesnt agree with the stock computer / tune. Im running the stock 55 mm behind my 70mm TB and the rest of a potentially 300 hp engine and its still not right.
4)You probably overpaid, however, i would glady have paid a few hundred more for my project and had the ability to just swap engines. It took me a long time to do the swap with the engine in the car, my back was always hunched over the fenders, and i had to be pretty meticulous about not dropping crud into the combustion chambers or the oil pan. Swappin the whole shabang wouldve chaved alot of time.
5)You can buy EGR compatable intakes. My 99 exploder engine had EGR ports in it and the bosses cast, but not drilled/tapped. I still have it if you want to buy it off of me. I ended up buying one that was looked over by Tom Moss. Try to sell your intake for one that is EGR compatable.
6)I have
BBK unequal shorties and they tight on cylinders 6, 7, and 8. Especially 7. Get P specifics if you can, otherwise, cheat like i did and do a temporary solution of flipping the spark plug wire around. Once they burn up my money tree should have sprouted a few more leaves for me to pluck.
