Chris, nothing on the body is square and both sides are not a mirror image so it just needs to look right on your car, don't try to be too perfect! Although you will know all the little bits that are wrong, everyone else will not notice when it is on the road.
So what I did......
1. Check the bulkhead is square with the frame and on the chassis first! Then bond the body onto the frame inside so it is in the position you want and will not move.
2. Use the bulkhead as the datum and try to match both sides so the bonnet shut lines down each side are approximately in the right place. Don't try to be mm perfect.
3. The important thing is the angle of the shut line as this needs to match the bonnet, so I measured about 2" back from the edge and drew a parallel line
4. Draw another parallel line about 3" back from the edge and this will give you 1" as the amount you will cut out. I extended both lines to the top of the body just short of the mould line on the top.
5. I then carried the 2" line from the top of the body to the centre of the body at the top and stopped in the middle. The 3" line then got drawn to meet the 2" line in the middle so you have a wedge shape. This allows you to keep the bonnet line from the middle and basically bend the top part back to meet your new line when you have taken an inch out of the side.
6. I then cut out the band of 1" down the side and moved that section back, pinning it with some little brackets - these were just kitchen unit right angle brackets that were flattened. Remember to leave a 2-3mm gap so you can get some bonding paste in the gap.
7. Cut your wedge out of the top so you can adjust it to meet the new shut line, I used a bracket along the shut line where the two bits meet to keep it all straight.
8. Once you are happy with it all, then whack some bonding paste in and some matting underneath when you can reach. The side will be supported by the paste you put in to close the gap between the bonnet and the bulkhead so that will keep it all solid.
The only thing to bear in mind is that since I have modified the body, I am expecting to have to adjust the bonnet to fit, as I expect it now to be an inch short on the passenger side.
From talking to others and seeing a couple of finished cars, some body's fit better that others and to be honest, I have only noticed the difference from side to side as I and looking for it, no one else will notice it! Make it fit as best you can but don't try and get it perfect as it will start to have a knock on effect with other stuff!
Good luck.