Change SSL certificate for server.

I Installed the system using the Perfect Server Debian Wheezy making a couple adjustments for Jessie (testing). When I set it up initially, I used a self-signed SSL certificate for the server functions. I now have an SSL class 1 from StartSSL and I would like it to replace the self-signed. I followed the directions https://www.howtoforge.com/securing...h-a-free-class1-ssl-certificate-from-startssl but afterward I get an Incomplete chain and Pure-FTP will not start. (Changing SSL certificates is easy on client sites, I wish there was a similar easy way to change the server's main certificate.) What did I do wrong? StartSSL gives these directions for Apache https://www.startssl.com/?app=21 but when I try to track doen the listed config files they don't exist or have been altered by ISPConfig3. What should I do?

Thanks.

Code:

root@abacus:~# cat htf_report.txt | more

##### SERVER #####
IP-address (as per hostname): ***.***.***.***
IP-address(es) (as per ifconfig): ***.***.***.***
[INFO] ISPConfig is installed.

##### ISPCONFIG #####
ISPConfig version is 3.0.5.4p5


##### VERSION CHECK #####

[INFO] php (cli) version is 5.6.4-4

##### PORT CHECK #####

[WARN] Port 465 (SMTP server SSL) seems NOT to be listening
[WARN] Port 21 (FTP server) seems NOT to be listening

##### MAIL SERVER CHECK #####

[WARN] I found no "submission" entry in your postfix master.cf
[INFO] this is not critical, but if you want to offer port 587 for smtp connections you have to enable this.
[WARN] I found no "smtps" entry in your postfix master.cf
[INFO] this is not critical, but if you want to offer SSL for smtp (not TLS) connections you have to enable this
.

##### RUNNING SERVER PROCESSES #####

[INFO] I found the following web server(s):
        Apache 2 (PID 2313)
[INFO] I found the following mail server(s):
        Postfix (PID 2860)
[INFO] I found the following pop3 server(s):
        Dovecot (PID 2492)
[INFO] I found the following imap server(s):
        Dovecot (PID 2492)
[WARN] I could not determine which ftp server is running.

##### LISTENING PORTS #####
(only           ()
Local           (Address)
[anywhere]:41516                (1358/rpc.mountd)
[anywhere]:110          (2492/dovecot)
[anywhere]:143          (2492/dovecot)
[anywhere]:111          (1128/rpcbind)
[anywhere]:44241                (1358/rpc.mountd)
[localhost]:7634                (1453/hddtemp)
***.***.***.***:53              (1234/named)
[localhost]:53          (1234/named)
[anywhere]:22           (1239/sshd)
[localhost]:631         (2668/cupsd)
[anywhere]:55639                (-)
[anywhere]:31416                (11930/boinc)
[anywhere]:25           (2860/master)
[localhost]:953         (1234/named)
[anywhere]:1017         (1293/rpc.rquotad)
[anywhere]:17500                (4979/dropbox)
[anywhere]:17501                (4973/dropbox)
[anywhere]:445          (2526/smbd)
[anywhere]:17502                (4982/dropbox)
[anywhere]:17503                (4976/dropbox)
[anywhere]:993          (2492/dovecot)
[anywhere]:2049         (-)
[anywhere]:55778                (1358/rpc.mountd)
[anywhere]:45858                (1148/rpc.statd)
[anywhere]:995          (2492/dovecot)
[localhost]:10024               (2895/amavisd-new)
[localhost]:10025               (2860/master)
[anywhere]:3306         (2052/mysqld)
[anywhere]:139          (2526/smbd)
[localhost]:11211               (1248/memcached)
[localhost]10           (2492/dovecot)
[localhost]43           (2492/dovecot)
[localhost]11           (1128/rpcbind)
*:*:*:*::*:8080         (2313/apache2)
*:*:*:*::*:80           (2313/apache2)
*:*:*:*::*:43088                (-)
*:*:*:*::*:8081         (2313/apache2)
*:*:*:*::*:53           (1234/named)
*:*:*:*::*:22           (1239/sshd)
*:*:*:*::*:631          (2668/cupsd)
*:*:*:*::*:25           (2860/master)
*:*:*:*::*:953          (1234/named)
*:*:*:*::*:443          (2313/apache2)
*:*:*:*::*:445          (2526/smbd)
*:*:*:*::*:993          (2492/dovecot)
*:*:*:*::*:2049         (-)
*:*:*:*::*:995          (2492/dovecot)
*:*:*:*::*:38439                (1358/rpc.mountd)
*:*:*:*::*:10024                (2895/amavisd-new)
*:*:*:*::*:47242                (1358/rpc.mountd)
[localhost]39           (2526/smbd)
*:*:*:*::*:36747                (1358/rpc.mountd)
*:*:*:*::*:59691                (1148/rpc.statd)




##### IPTABLES #####
Chain INPUT (policy ACCEPT)
target     prot opt source               destination        

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination        

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination        



root@abacus:~#

 

my all OpenSSL, RapidSSL certificates me work etc
new certificates unless you have given me StartSSL not work or client mode