Debs - I wish I had read your post earlier.
You are absolutely right to be concerned, I think there are several issues here that concern me - I am not sure I would be removing my child so early - but totally accept that you know your child and make the decision that is right for you and your family - the fact that you feel so much better now he has finished indicates this.
Firstly - if the school had concerns re your child having any particular special needs then this should be addressed with you in a specific meeting about your child's progress - I would expect this meeting to be between you and the child's teacher possibly with SENCo present but probably a one to one initially. I would not expect HT to be involved in the early stages and if they were it would be with the class teacher not just on spec.
Secondly you are absolutely right to be concerned about a child coming home having had treatment in school for an injury with no documentation/info to parent.
Thirdly - if you are so concerned about the HT that you are taking your child out of the school then certainly the governing body should know about it. If you have raised concerns with the HT then they should address them with you.
Fourthly - you say the Chair of Governors is the SENCo - this cannot be so. The SENCo now has to be a qualified teacher, a teaching assistant may undertake some of the role but the responsible person for SEN/Inclusion must be a qualified teacher. The chair of governors cannot work at the school, so I don't see how your CoG can be SENCo. Many governing bodies will have a named governor responsible for overseeing inclusion/special needs but they really only feedback to the governing body on the way school manages SEN, work on policies etc. They don't get involved with specific children.
I think I would proceed along the following lines.
Email HT again asking for a reply to your previous concerns and give a cut off date (a week?). I would ask specifically for answers to your queries, what school policies say etc. I can't believe the school accident policy does not indicate that parents should be informed about injuries etc.
I would wait for the reply and consider whether it is adequate.
Regardless of whether it is adequate I would write formally to CoG identifying your concerns - be specific and highlight that the result of these concerns and them not being dealt with adequately is that you have removed your child from the school.
Whilst I accept that your HT may be relatively new to post, simply to become HT they should have several years of experience and be equipped with reasonable communication skills (yes I know many HT's out there completely lack them!). If this HT's communications skills are going to lose the school pupils then the Governing Body need to know about it so that they can set this HT some performance management targets to address this and the sooner they do so the better. No Governing body wants to find out that their HT is alienating parents only after they've lost a significant number of pupils and the message has go out to the local community why!
So write away - copy the letter to the LA (or diocese if your a religious school) and wait for a response. If you are not happy, particularly with an aspect of school safety then any parent has a right to contact ofsted directly and inform about their concerns.
Good luck - plese don't just leave it now your child has left - there are lots of other parents and children (and staff)under the care of this HT