This does all sound very chaotic and perhaps your Clerk and Chairman would benefit from specific training in this regard, which is readily available.
There is no justification for routinely over running a meeting and your time limit of 3 hours is on the generous side. Many councils opt for a shorter limit. All items on the agenda must be fully explained to the public beforehand and the only realistic way to achieve this is to follow the model that has been used by larger authorities for as long as I can remember. Written reports, published a few days in advance of the meeting (Transparency Code), taken as read at the meeting, one question per member, clear recommendations in the report, vote by show of hands, move on.
For my own Parish Council, the one I Chair rather than Clerk, we have a simple report template, with three headings: Purpose of Report, Key Issues, Recommendations. This is used for every item on the agenda. Purpose, obviously, explains the reason for bringing it to the council. Key issues, usually bullet points, explains the background, essential information and proposed actions. Recommendations provides specific resolutions to be voted upon and for the Clerk to include in the minutes. Reports must be with the Clerk a week before the meeting to appear on the agenda. There are two main sections of the agenda: Reports for Information and Reports for Decisions. In the case of an information report, the recommendation is simply "Members note the contents of the report." As stated above, at the meeting, I introduce the item, ask the report author whether there is anything they wish to add to the report, invite questions from members, read out the recommendations, request a show of hands, then move on to the next item. We allocate three minutes for a decision item, less for an information report. Occasionally something will take a little longer, but they average out over the course of a meeting. It's not unusual for an information report to be done and dusted in 30 seconds, when it would have taken ten or fifteen minutes previously. We have no oral reporting, urgent items must require an urgent resolution in order to be included and we have no any other business. A typical agenda would contain up to twenty reports, for which a couple of hours is adequate, including a public forum.
It wasn't popular with members when we introduced it, as some liked the sound of their own voices, but it has gradually been adopted by the majority. New councillors just accept it as the only way. It means that Mrs Biggins from No 42 Acacia Avenue can visit the website the day before the meeting to find out whether or not we're discussing anything that has a bearing on her life, to allow her to decide whether or not to attend. That's what the Transparency Code is all about.