Built in Apache removed

I have removed the Stock version of Apache because of several configuration issues I could not get past. I have installed a new version of Apache and all config files are now in different locations than stock. After setting up web services in Mds I realized that all the config files are being placed in the stock Apache locations. My question is it possible to get Mds Web service to work with my current working version of Apache and the different locations for the config files? Thanks in advance for any assistance.

If you are running your own webserver, I recommend that you manually set up the other services (MunkiReport / Munki). The project sites for each shows how to set it up with apache.