Most of your PHP3 application should work with PHP4 so I really don't see the need for both.
However,
Get the latest version of PHP4.
Modify the PWS-php4.reg ...
e.g.
####
REGEDIT4
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\w3svc\parameters\Script Map]
".php3"="c:\php3win\php3*.dll"
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\w3svc\parameters\Script Map]
".php"="c:\php4win\php4*.dll"
#####
Then see if you can merge the php.ini..
--- This will be the trick!!!
Are you using all the *.dlls that came with each version?
If not you maybe able to mix the dlls.
for example, if you don't have sql70 leave out the PHP4 sql70 dll and continue to use the php3 sql65 dlls.
HTH
Chauncey