I think you want the first cert after the RSA stuff. If you want the 2nd cert, then some fiddling required.

#!/usr/bin/perl -w
use strict;

my @cert;
my $flag=0;
while (<DATA>)
{
   $flag =1 if /END RSA PRIVATE KEY/;
   if ($flag and my $f=(/BEGIN CERTIFICATE/.../END CERTIFICATE/))
   { 
      push (@cert, $_);
      #print "$f\n";  #to see what that does
      last if ($f =~ /E0$/); #skip other following certs
   }
}

print @cert;
=prints
-----BEGIN CERTIFICATE-----
AAAAijCCA/OdfsdasdfsdfsdfsaavZsdfEeEEdV9/sdfsdfsdfsdfaaasdfwerfd
ujEfMB0dfgsdfgsdfgsdfgNpZ24gVHJ1c3QgTmV0d2sdfgsdfgUGA1UECxMOhh5y
aVNpZsdfgsdfgy4xMzAxBgNVBAsTKlZlcsfggdfuIEludGVybmFsdfgsdfggU2Vy
dmVyIENBIC0gQsdfgsdfgzFJMEcGA1UECxNAd3d3LnZlcmlzaWduLmNvbS9DUFMg
SW5jb3JwLmJ5IFJlZi4gfgsdfgsdfgsdfgxURC4oYyk5NyBsdfgsdfgnbjAeFw0x
MDA3MjkwMDAsdfgsdfgsdfA3MjkyMzU5NTlaMIGaMQswCQYDVQQGEwsdfgsdfg4G
A1UEsdfgsdfgaGlhbjESMBsdfgsdfgQJRWRpbmJ1cmsdfgsdfgYDVQQKFCRUaGUg
Um95YWwgQmFuayBvsdfgsdfgsdfgZCBHcm91cCBQbGMxFDASBgsdfgsdfglUIFNl
Y3VyaXR5sdfgsdfgVsdfgsdfgnsdfgsdfgsdfgsdfgssdfgsdfgvbTCBnzANBgkq
hkiG9w0BAQEFAAOBjQAwgYkCgYEAlj/N+i5KafA5LDsZlsB7RxKAOz7rpx2UHkqD
usdXugRxcioSiG0KPJp45NAT+TPkkbw2Sdfq6G86WKGbERzAZUtUNNjxSdwssdfF
y6sdC/5sdfsdfsaadsf4V6YK03gsx/7rjsdfasdfasdfasdfv8srsO+jadfYzE/s
ddilRP0CAwEAAaasdfasdfGpMAkGA1UdEwQCMAAwasdfasdfasdfAgWgMasdfasd
HwQ1MDMwMaAvsdfoC2GK2h0dLy9TVlJJbnRsLWNybC52ZXJpc2lnbi5jb20vU1ZS
SW50bC5jcmwwRAYasdfasdfDOzA5BgtghkgBhvhFAQcXAzAqMCgGCCsGAQUFBwIB
FhxodHRwczovL3d3dy52ZXJasdfasdfpc2lnbi5jb20vcnBhxxQhMB8GCWCGSAGG
+EIEAQYIKwYBBQUHAwEGCCsGAQUFBwMasdfCMsdfsdfsdfaaawUwYzAkBggrBgEF
BQcwAYYYaHR0cDoasdfasdfyaXNpZ24asdfuY29tMDsGCCsGAQUFBzAChi9odHRw
Oi8vU1asdasdfasdfkj;s8sdkdkdkdkdduY29tNWUkludGwtYWlhLmNlcjBuBggr
BgEFBQcBDARiMGChXqBcMFasdfasdflpbWFnZS9naWYwITAfMAcGBSsOAwIaBBRL
a7kolgYMu9BasdfasdfHiyEFGDAmFiasdfasdf8vbG9nby52ZXJpc2lnbi5jb20v
dnNsb2dvMS5naWYwDQYasdfasdfNAQEFBQADgYEAXMaMasdfasdff1r64zrglX6d
XQPu3asdfasdfLEgMN+asdfbasdfrjpasdfasdfq7CCcm2PU50u/Xasdfasdfxfw
hDYTIbKIPQP+hjsK47dtc+7X4aKYasdfkuMrFmhwokjIDgasdfasdfwhv2TrvRej
fHuaARasdfasdfoTiCc=
-----END CERTIFICATE-----
=cut


__DATA__
adsfaFD DSAfds
-----END RSA PRIVATE KEY-----
Bag Attributes
    localKeyID: 00 00 00 00 00 00 00 00 00 00 00 00 00 
    friendlyName: my.site.here.com
subject=/C=US/ST=Here/L=NC/O=My Org/OU=Security/CN=my.site.here.com
issuer=/O=VeriSign Trust Network/OU=VeriSign, Inc./OU=VeriSign Interna
+tional Server CA - Class 3/OU=www.verisign.com/CPS Incorp.by Ref. LIA
+BILITY LTD.(c)97 VeriSign
-----BEGIN CERTIFICATE-----
AAAAijCCA/OdfsdasdfsdfsdfsaavZsdfEeEEdV9/sdfsdfsdfsdfaaasdfwerfd
ujEfMB0dfgsdfgsdfgsdfgNpZ24gVHJ1c3QgTmV0d2sdfgsdfgUGA1UECxMOhh5y
aVNpZsdfgsdfgy4xMzAxBgNVBAsTKlZlcsfggdfuIEludGVybmFsdfgsdfggU2Vy
dmVyIENBIC0gQsdfgsdfgzFJMEcGA1UECxNAd3d3LnZlcmlzaWduLmNvbS9DUFMg
SW5jb3JwLmJ5IFJlZi4gfgsdfgsdfgsdfgxURC4oYyk5NyBsdfgsdfgnbjAeFw0x
MDA3MjkwMDAsdfgsdfgsdfA3MjkyMzU5NTlaMIGaMQswCQYDVQQGEwsdfgsdfg4G
A1UEsdfgsdfgaGlhbjESMBsdfgsdfgQJRWRpbmJ1cmsdfgsdfgYDVQQKFCRUaGUg
Um95YWwgQmFuayBvsdfgsdfgsdfgZCBHcm91cCBQbGMxFDASBgsdfgsdfglUIFNl
Y3VyaXR5sdfgsdfgVsdfgsdfgnsdfgsdfgsdfgsdfgssdfgsdfgvbTCBnzANBgkq
hkiG9w0BAQEFAAOBjQAwgYkCgYEAlj/N+i5KafA5LDsZlsB7RxKAOz7rpx2UHkqD
usdXugRxcioSiG0KPJp45NAT+TPkkbw2Sdfq6G86WKGbERzAZUtUNNjxSdwssdfF
y6sdC/5sdfsdfsaadsf4V6YK03gsx/7rjsdfasdfasdfasdfv8srsO+jadfYzE/s
ddilRP0CAwEAAaasdfasdfGpMAkGA1UdEwQCMAAwasdfasdfasdfAgWgMasdfasd
HwQ1MDMwMaAvsdfoC2GK2h0dLy9TVlJJbnRsLWNybC52ZXJpc2lnbi5jb20vU1ZS
SW50bC5jcmwwRAYasdfasdfDOzA5BgtghkgBhvhFAQcXAzAqMCgGCCsGAQUFBwIB
FhxodHRwczovL3d3dy52ZXJasdfasdfpc2lnbi5jb20vcnBhxxQhMB8GCWCGSAGG
+EIEAQYIKwYBBQUHAwEGCCsGAQUFBwMasdfCMsdfsdfsdfaaawUwYzAkBggrBgEF
BQcwAYYYaHR0cDoasdfasdfyaXNpZ24asdfuY29tMDsGCCsGAQUFBzAChi9odHRw
Oi8vU1asdasdfasdfkj;s8sdkdkdkdkdduY29tNWUkludGwtYWlhLmNlcjBuBggr
BgEFBQcBDARiMGChXqBcMFasdfasdflpbWFnZS9naWYwITAfMAcGBSsOAwIaBBRL
a7kolgYMu9BasdfasdfHiyEFGDAmFiasdfasdf8vbG9nby52ZXJpc2lnbi5jb20v
dnNsb2dvMS5naWYwDQYasdfasdfNAQEFBQADgYEAXMaMasdfasdff1r64zrglX6d
XQPu3asdfasdfLEgMN+asdfbasdfrjpasdfasdfq7CCcm2PU50u/Xasdfasdfxfw
hDYTIbKIPQP+hjsK47dtc+7X4aKYasdfkuMrFmhwokjIDgasdfasdfwhv2TrvRej
fHuaARasdfasdfoTiCc=
-----END CERTIFICATE-----
Bag Attributes
[download]