It is not possible to write a standard letter for this confirmation as every case will be different.
What is required is that you are gathering evidence to support your decision on employment status.
For each factor that you wish to rely on the best approach is to write to each party, the client and the agency for you to confirm how you understand the relevant contractual and working practices to be, and to request that they agree that your understanding is correct.
You may find that they do not reply, in many respects this does not matter, as long as you have written to them explaining how you see the matter then this should help you in defending your employment status.
Some example paragraphs maybe:-
1. My understanding of clause 3.14 is that should I be unable to complete my assignment on a particular day I may send a nominated substitute to complete my assignment, and that I will be responsible for the costs of this. I can do this, but will refer to you beforehand if this is the case, and that you will not withhold your consent unreasonably.
2. As I am a specialist in the area of xxxxxx my understanding of this contract and the clause in 3.17 is that I will complete my assignments within this contract using my specialist skill an knowledge but within the time frames required by the project. As such my reporting to your client XXX will be only as far as delivery times are concerned.
3. I understand that if the client xxxx has no further requirement for my specialist skills that this contract will terminate within a 7 day period, this period to allow me to handover any relevant details to the client and allow business continuity. In the event of this happening you are under no obligation to find me any further work and I am free to seek alternative work from other sources.
4. I have detailed my understanding of my contract between yourselves and my company and will be basing my tax compliance on this and other correspondence that we have had. My understanding is that you have no conflicting clauses or arrangements with your client and I ask you to confirm this to me