Some modifications from stock are expected. Things like configuring your instance with your specific settings for the sites, departments, teams, help topics, ticket statuses, etc.
If it were me... I would download the core source files for the version that you are running. I would then us a diff utility to find the differences between your modified version and the unmodified one. I would document the changes. I would then setup a current version test site and would assess if those changes are actually needed compared to the current version of osTicket. If not I would upgrade. If so then I try to recreate the mods on the current version test site.
That being said...
lisareed At this point we would like to streamline the departments and update our help topics. what are the ramifications of doing this to a live system in use?
I personally do not delete Departments in my production sites. I do rename them and set their Status to Disabled.
I do the same with Help Topics. Doing this simply means that tickets cannot be routed to that department via help topic , ticket filters, etc.
lisareed if we delete several help topics - and add in new ones, what happens to existing topics currently under the old help name?
Since that information is stored in the ticket (ost_ticket table) I imagine that it would not let you delete the Department/Help Topic/Team while there are tickets assigned to them. I haven't actually tried to delete either in a dogs age. None of our production sites utilize teams.
Something to think about though is if you remove Department access to Agent then no agent will be able to access the tickets that in that department. If it were me, I would go through all my Help Topics (and Ticket Filters) and make sure that none of them send tickets to the old department (by disabling them) and then I would disable the Department. I would setup the new Department and Help Topics to send new tickets to those. And I would add that Department to the access of the Agents that need them.
I'm not caffeinated yet today, so I hope that all makes sense. If it doesn't, or if you have another question please feel free to reply. I'm here until 3pm EST today.