It's a long drawn out process with lots of shouting and tub refitting!
The rear bumpers are the key to lining it up, this page pretty much covers what we did with bumper fitting:
http://www.msportster.co.uk/detail.asp?cat=10&offset=60 - the spare wheel well does not sit on the chassis, its up a bit
As for the length of the doors, have you got the striker plates from Marlin? The one welded to the chassis need to be cut back - a lot. Then the new striker plates bolt on further back than the originals. The front of the tub needs the bottom trimming down to fit. I had trouble with the angle on the passenger good so I ended up putting a rivnut on the striker plate combined with a counter sunk bolt and cup washer which helps pull it in line.
The doors, which I though were wrong originally were not as wrong as I though. I though they had to be flat, which they didn't. They need to be bent in towards the car a bit at the top rear. My ones didn't match, one was not in as far as the other. So I had them straightened out. After switching the striker plates and moving the tub further back the doors needing bending again.
You can see the striker plate rivnuts here:
http://www.msportster.co.uk/detail.asp?cat=10&offset=72
The drivers door was scraping on the tub ever so slightly (you can see the mark in the pictures on the page above) I fixed this with a bodywork hammer. Just tapped the edge until it went right past