You appear to be making allegations of improper conduct against an elected member of your district council. The correct avenue for this is to report these matters to the monitoring officer of your district council and I would advise you to do this without delay. However, I advise you to be more focused in your reporting, concentrating solely on the matters which you believe relate to misconduct in public office. Self-promotion and granting of non-pecuniary favours are an everyday part of political life, whether we approve of them or not. If the monitoring officer determines that further investigation is required, or that criminal offences may have been committed, they will take the necessary steps to pursue this. Toothless they are not!
Dealing with some of the specific matters individually, registered charities must operate independently and are not subject to public scrutiny in the way local councils are. As long as they are complying with the Charities Acts, they are doing nothing wrong. If the parish council owns the village hall, it is right and proper that it should provide for current and future maintenance where this is necessary. The wording of the legal agreement between the two parties should define this responsibility and this usually forms the governing document of the charity. I would hope that the parish council took appropriate legal advice regarding the development of the app, but regardless of this, if the internal auditor has seen the details of this and raised no concerns, the implication is that it does not contravene any legislation.
The Clerk is free to take up any paid employment alongside their parish council role. It is not uncommon for parish council clerks to work for other councils, churches, parish charities etc and there are many benefits to the community in doing so. If you feel that minutes of parish council meetings are not an accurate reflection of the business of the meeting, you should raise this with the members of the council and the Clerk. You have the right to record all parish council meetings to provide you with the necessary evidence of inaccuracies or omissions, but please bear in mind that the minutes are not intended to be a verbatim account of everything that was said at the meeting. All business of the parish council should be conducted in the public domain, so I can't think of any confidential information that could be passed to a district councillor that they do not already have access to by virtue of that position. If the village hall charity resolves that it is in the best interests of the charity to engage a paid employee, that is a matter for them. The same is true of the village charity.
I'm surprised that the Section 106 money is being diverted into the village charity, but there is no obvious legal impediment to this. My initial thought is that, depending on how it will be utilised, there may be a VAT cost to this.
The whole situation sounds messy and from what you have said, the basic democratic principles have been manipulated to benefit the reputations of the few. However, the public lethargy you refer to may, in part, be due to the fact that people appreciate the provision of their new villlage hall and the other services and amenities that have been spawned by this shenanigans.