(http://localhost/Certsrv ) errors page cant be found with 404

Open cmd and run certutil.exe. Post the result.

C:\Users\Administrator>certutil
Entry 0: (Local)
  Name:                         `davidfoxtranspo-DATA-SERVER-CA'
  Organizational Unit:          `'
  Organization:                 `'
  Locality:                     `'
  State:                        `'
  Country/region:               `'
  Config:                       `DATA-SERVER.davidfoxtranspo.local\davidfoxtrans
po-DATA-SERVER-CA'
  Exchange Certificate:         `'
  Signature Certificate:        `DATA-SERVER.davidfoxtranspo.local_davidfoxtrans
po-DATA-SERVER-CA.crt'
  Description:                  `'
  Server:                       `DATA-SERVER.davidfoxtranspo.local'
  Authority:                    `davidfoxtranspo-DATA-SERVER-CA'
  Sanitized Name:               `davidfoxtranspo-DATA-SERVER-CA'
  Short Name:                   `davidfoxtranspo-DATA-SERVER-CA'
  Sanitized Short Name:         `davidfoxtranspo-DATA-SERVER-CA'
  Flags:                        `13'
CertUtil: -dump command completed successfully.

Do you see the certserv virtual directory in IIS? and also make sure that you have installed the AD webservices.

the Virtual Directory is in the IIS , the Physical path exists c:\windows\system32\Certsrv\en-us
when you run the test under Basic settings it fails on Autherization can not verify path (path as above)

if you test using browes this is the result
Error Summary
HTTP Error 404.0 - Not Found
The resource you are looking for has been removed, had its name changed, or is temporarily unavailable.
Detailed Error InformationModule
IIS Web Core
Notification
MapRequestHandler
Handler
StaticFile
Error Code 0x80070002
Requested URL
https://localhost:443/CertSrv
Physical Path
C:\Program Files\Windows Small Business Server\Bin\WebApp\SBS Web Applications\CertSrv
Logon Method
Anonymous
Logon User
Anonymous
Most likely causes:•The directory or file specified does not exist on the Web server.
•The URL contains a typographical error.
•A custom filter or module, such as URLScan, restricts access to the file.

I think your problem is dns.  If you go to command prompt and do no lookup localhost what does it return?

a ns lookup fails

IN application pool -> advanced settings, enable 32 bit made is false or true? if it is false then make it true
was set to false now set to true

Try this:

https://DATA-SERVER.davidfoxtranspo.local/Certsrv

looking in the IIS I have noticed the default web Site has a ? when I check it the manage web site it does appear to be started , when I click start an error comes up saying :-
Default web site cannot be started another web site is using the same port

it has a SBS site running that does use both port 80 and 443 has well

is this possible the problem.

https://DATA-SERVER.davidfoxtranspo.local/Certsrv
gives error server not found

The SBS site is correct.  It might be helpful to understand exactly what it is that you are trying to accomplish with the cert server and then we can provide better solutions.  SBS has some unique configurations

we have updated the pc's and office software so now the email system wants to use Certificates
we have now created some new certificate and we were trying to self sign them using the CA on the server this is when we found the Certsvr would not run

Can you check the services related to certificates are running.

So, to create Self Signed certificates in an AD where you have SBS running, you are to use the Wizard in the SBS console.   Are you running SBS 2008 or 2011??

SBS2008 in this case

This blog article from the Microsoft SBS team will explain how to create a new self signed cert using the wizard in the SBS Console and then how to distribute the cert for external users

https://blogs.technet.microsoft.com/sbs/2008/09/30/how-do-i-distribute-the-sbs-2008-self-signed-ssl-certificate-to-my-users/

I have read this article only talks on how to distribute the certificate, , I got the Certificate created just need to certify them using CA

You might have skipped over the part that says...."create a new self-signed SSL certificate through the Internet Address Management Wizard (IAMW)"   The Internet Address Management Wizard (IAMW) is found on the Getting Started page of the SBS 2008 Console