Here is my draft, I have included all points that are not subjective. Thanks Again everyone! 
Dear Sir/Madam
Ref: PCN Number: GX09900630
My grounds of my appeal are that:
The contravention alleged by the Authority on the Penalty Charge Notice did not occur.
1. Paragraph 7(1) of Part II of Schedule 19 to the Traffic Signs Regulations and General Directions 2002 provides
that no person shall cause a vehicle to enter a box junction so that the vehicle has to stop within the box junction
due to the presence of stationary vehicle. The councils evidence does not show my vehicle entering the Yellow Box Junction. And the offence is completed at entry of the YBJ which is not shown. London Tribunal case 2130491073, 2160264616, 2230099245
2. The top left hand corner of the box does not meet the kerb line. In the absence of any special authorisation that this box is compliant with either diagram 1043 or 1044 of The Traffic Signs Regulations and General Directions 2002. Therefor this PCN is unenforceable. London Tribunal case: 2110069641, 2110138201
3. The PCN states I committed the offence at 17:26 whereas actually it must have been no later than 17:25, But this cannot be verified due to my entry not being on the CCTV.
4. The PCN states contravention code 31. However this is captured on CCTV so the code should be 31J.
The TSRGD 2002 has been updated by the TSRGD 2016 which, as I understand, has given more wiggle room around the placing of the box junction markings. As such, I'd be inclined to remove point 2, for fear of giving an adjudicator the impression you are fishing and subconsciously turning them against your other arguments which (while they have merit) are also subjective and require the adjudicator to be on your side to prevail. I note the two cases cited are from 2011 which is before the revised regulations came into force.
I also think the 31 vs 31J code argument is weak so have suggested removing (but you can reinstate if others think it's a potential winner)
Suggested redraft (wait for other comments)
Ref: PCN Number: GX09900630
I contend that the contravention alleged by the Authority on the Penalty Charge Notice did not occur. My representations are as follows:
1. Under the relevant box junction regulations no person shall cause a vehicle to enter a box junction so that the vehicle has to stop within the box junction
due to the presence of stationary vehicles. I have reviewed TFL's video evidence and it does not show the moment my vehicle entered the box junction. There are numerous tribunal decisions which confirm it is a requirement for the video evidence to show the moment of entry into the box (including a key case on the London Tribunals website). Further London Tribunal cases setting out this principle are 2130491073, 2160264616, 2230099245.
2. The PCN is required to state the grounds on which a penalty charge is payable. To this end the PCN states the time the alleged offence was committed as 17:26. Under the relevant box junction regulations, the offence is committed at the point of entry into the box (the actual offence is causing a vehicle to enter the box if it subsequently has to stop within the box junction due to the presence of stationary vehicles). As set out in my first point, the video footage does now show my vehicle entering the box and so it is not possible to know the time the alleged offence occurred. Taking the time stamp on TFL's own footage at face value all one can deduce is that the vehicle entered the box junction no later than 17:25 as it can already be seen within the box junction at this time. As such the grounds stated on the PCN are shown to be incorrect by TFL's own evidence and the contravention as stated on the PCN clearly did not occur.
