FERC recommended of using a Rp of 3 for Cat II piping in seismic design, as a result there is a huge acceleration of 4.6 which is not real for the geographical area that I am working on, would any body have any ideas of how to deal with FERC numbers?

I do not believe an Rp of 3 for B31 piping is too small. While ASCE 7 lists Rp=12 for such piping, B31E says Rp shall not exceed 3.5 when used with the allowable stresses found in that document.
But 4.6 g is huge. What does the rest of your horizontal acceleration equation look like? (Note that the equation uses Sds, not Ss.)

Thanks Dave,this is how my data looks like:

aP Component Amplification Factor 2.5
IP Importance Factor 1.5
Rp Component Response Modification Factor 3.0
SS Mapped MCE Spectral Response 0.426
S1 Mapped Spectral Response Acceleration at 1sec 0.127
SDs The Design spectral response acceleration at short periods 0.44
SD1 Design earthquake spectral response acceleration parameter for 1st second 0.251
aH Seismic Acceleration 0.66

aH,Final Design Horizontal Seismic Acceleration 0.46

So your 4.6 is now 0.46?
When I use your data the seismic wizard in CAESAR II, I get 0.435.

Oh Sorry my bad!
I meant 0.46.
I think for the eastern USA, 0.43 looks high.