None of the following is a substitute for obtaining professional advice specific to your council.
If your council does not have an adopted grievance procedure, then I would suggest adopting one as soon as possible. It's an essential part of the management of employees, and there are plenty of models around. Then you should follow the grievance procedure.
It's quite likely that you will need to copy the grievances and related documents, although as a council, you are entitiled to find someone who will do the copying for you at the council's expense.
Another thing to do immediately is to check whether the council has an insurance policy, and if so, whether it covers legal support for employment disputes. If it does, you may be able to obtain the services of a solicitor without incurring costs for the council.
Although local councillors are unpaid volunteers, councils are still subject to the full force of employment legislation. Disputes can become extremely expensive - it is by no means unknown for a dispute with a clerk to cost £20,000 before it is resolved. Dealing with an employment dispute may also take many hours of councillor time. Although this seems an unfair burden on volunteers, it is what happens.
In general, painful though it may be, it is advisable to make every effort to avoid the council being in the wrong in its dealings with the clerk, however much you may feel that the fault lies with the clerk. Avoid discussion of contentious matters outside formal meetings, ensure nothing is done by a sole councillor (even the chairman) and try to give the clerk no possible grounds for complaint.
If you think the situation is not going to be resolved by agreement, then the council really does need to obtain legal advice and to follow it carefully.