After having a play around today I came to the conclusion (which I had i think decided on a while ago) to restart. My reasons for doing this are that as I have gone along I have realised that errors with the shapes of the walls were going to cause me a lot of trouble later on with rendering and a lot of what I had done had been hacked together a bit as I had gone on to just make it work. The final realisation was that I realised that the reason I was having issues lining up the survey data with my walls was because I had forgotten the walls are not straight! This has come from me remembering (albiet a bit late) that the way medieval ceilings/ floors are constructed is based on *balancing* the edges of beams on an overhang. the following image shows the east elevation and the more mossy strips of masonry show where the line of bricks at the top of each floor before the wall falls back.
So I have started from scratch again to make sure I include this. I started by importing the survey data again but this time grouping it all together and moving it to (0,0,0) as well as aligning it to the grid. This should make future modelling easier than it has been as x,y,z now should be moving either along, into or up the walls of the elevation. I next imported the wall file I had used before which was constructed of basic shapes such as extruded rectangles to create the space of the rooms. I deleted all but the main rectangle as I decided until I had lined everything up and generated the right shape for this basic space there was no need to try and create the tower rooms as they would probably need editting at a later point anyway. I then shrank the wall down to just the basement level. I then created a copy of this shape by selecting and moving along the x axis, than had to just extend it to the right position. I then selected the polygon of the wall and moved this backward to make the wall thinner and generate the step on which the floor would stand. I did this again to create the 2nd floor. This has solved all the problems I was having trying to line up the window guidelines on different levels.
I am now going to start modelling the window on the lower floor. I think this time I will try a slightly different method for creating the right shape as I realised the method I was using wasn’t generating the most even shape.