From what I understand you will gain about 50 hp right off the start and no you cannot use your stock intake; the lower intake for the 351 is wider and I don't think the headers will clear either. You will also need a new oil pan.
The speed density will give you problems so you will need a mass air conversion.
Yes you can use your stock fuel injection.
The t-5 will hold up as long as you are not too abusive on it but any time your power shifting a stock t-5 you take a chance on breaking it.
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James Cox
nochevy@hotmail.com
1991 Mustang LX
12.565 @109.38mph 1.764 60ft