Going .060 0ver on a 979xxxx or 481988 400 is generally not considered the best thing to do if you're building a performance engine, but if you have the cylinder walls sonic checked first for thickness and it's okay then you can do it. Of course, it's not as strong as a virgin 400 block being bored and honed for the first time, but those are getting harder and harder to find these days.
I went w/ .020 over Probes for my 455 since they were available and my 455 block was still standard- no point going .030 over when going .020 over would clean it up.
Geno