Hi Paul,
I have been studying my build manual this afternoon, and have noticed somthing with the drawings that may be misleading you.
On pages 9 & 10, it looks as if the body is longer than it actually is, and that the seat is farther forward, this is not the case.
Treat them as 'Illustrations', and not true representations of the finished car.
As you say the rear corners of the seat base encroach slightly into the top corners of the wheelarch apertures, mine's the same, (but not as much as yours) and I solved it by 'Chamfering' them down to make them less noticable (only I saw them, but it annoyed me).
The sides are a worry, but if you've followed the instructions in the build manual, they should be the same as everyone elses.
I would like to bet that the battens placed onto the body sides are the problem.
I found that the battens on the cars sides, seemed to be in the wrong places, so I placed them when I was happy the body was lined up correctly.
I took all of the battens off the sides, turned the tub on it's side, placing the side on top, and fit the sides 'by eye', aligning the front end first with the aid of a large set square hanging down across the body, before clamping it into place (loosely), before aligning the back end.
Don't forget that on the outer (body) side, the wing top sits FLUSH with the top, and sits ON TOP of the Inner Wing panel, so a piece of scrap timber is needed on top of the Inner Wing, to get the alignment right.
Once you are totally happy with the alignment of the sides,
then mark the position of the battens, Front Bulkhead (No 2), Floor Edge (No 3), Riser (Extra), with a pencil, and attach them with the aid of your Set Square. The batten for the riser fits
'In-between' the top and bottom battens on the riser, but screws to the
body. I used it as a 'Location' device, but it can be screwed to the riser (after final assembly) for extra strength if required.
This will give you an 'Interferance Fit' of the panels, and they can be positioned for test fitting without screws. Note, the TOP of the Floor batten is 2 inches above the lower edge of the Body Side, roughly level with the sill line.
This is how I found the 'Warping' in the floor panel, and once this was sorted, things came together easier.
As for the front Skirt / Valence, it was my interpretation that it seemed to fit below the edges of the wings, filling the slight gap at the bottom of the inner edge, before being held in place with panel pins. But I have just looked at the build manual again, and it would appear that your method is correct, and I was Wrong!
I do recall having to re-position the fixing batten slightly lower down on the front panel, to get the skirt / valance to fit properly, so this is probably why.
I appologise to Richard, as it seems that I am attacking his plans, but I know that this problem is not of his making.
You may not be aware, but Richard 'Inherited' the plans when he bought the company some years ago, so changes are going to be gradual, but they are coming. [2009]
Like we have said before, try to assemble the parts and make adjustments as you go. When you succeed (as we know you will), then you will be inducted into the 'I built mine from patterns' club, and all will be doubly impressed!

Keep Smiling,
Best Regards,
Mark.