Right cracked it... The seals that were in there weren't put in correctly so I was following the wrong pattern. After some more swearing and then checking eBay to see if anyone was flogging the both sides with seals in situ I thought I'd better work it out...
For anyone looking at this down the road... Here's how to fit (perfectly) in under 10 minutes (let's just pretend the "investigatory" first 4 hours never happened

).
The seals are handed so avoid mixing them up, if you do the vertical edge has a flap - that bit faces to the inside of the car. At the top of that piece is a triangular section
Looks at the seal there are two parts at the business end of things that make contact with the window chrome.
You'll see a short edge and a bit that looks like a flat tyre i.e. bulbous at the end.
The short edge along its length goes on the outside of the chrome i.e. facing into the car. Don't let this go into the groove of the chrome or it fs things up.
The bulbous part goes in to the groove and fills it either side.
Start with a corner of the vertical and get the bulbous part on the groove and the short edge in position all the way around the window chrome.
There are only 3 things that matter. 1 getting it right at each corner. 2. Same with the pointy end of the window 3 Making sure the short edge doesn't fall in to the groove
Start with the top corner of the window pull the seal and seat it as best as you can making sure it's on the corner. Same with the bottom corner. Don't worry you'll get these in snug in a bit.
Whilst you're doing this the seal at the pointy end is going to try and make a run for it. Get it back in place
Next... Take whatever you can find under the kitchen sink.. I used Dettol whatever cleaner. Give the the bulbous part a squirt along its length (you can only get to one side at this point... this should be facing outward from the car).
Give the the top of the seal a squirt too... This is important
Stand above the window looking down at the vertical side. Using your thumbs you're going to want push down on the part above the bulbous bit (it's got three lines on it and your thumbs will know when it's on it as the bulb end against the groove will resist).
Push down hard and when it seats you'll feel it.
Now shove your thumbs down the top edge (that's why you spayed it, so they can move unhindered) pressing as you go seating the full length.
The corners that may not have gone yet on either side. Use the same technique as above.
Make sure the short edge hasn't gone in to the groove of the vertical. (If the bulbous end has seated it can't be in but check anyway as it may have gone in at the corner, if it has fetch it out with a plastic trim tool).
Next go to the top edge of the window. If you're seated it correctly on the vertical edge and corner AND the short edge isn't in the groove this is going to go in quickly.
Making sure the short edge is still facing inward to the car and not in the groove many your way to the pointy end of the window.
It's going to want to pop out from the groove you've rested it on as you're doing the above so you'll want to keep it in place the bit of tape idea came in handy
Now do the same with the bottom edge
If your corners are in square the position of the seal on the pointy bit sorts itself out.
Now do the pointy part. The seal will fight you all day long if you try and stuff it in because of the tension caused by the rest of the seal being in place.
Making sure the short edge is still not in the groove pull the toppest edge of the seal down towards the vertical edge and the bulbous end will fall into the groove.
At the pointy end there may be some ripples in edge of the seal because if how you fitted it and it may not be in the perfect position. Just push the seal in the groove one way or the other and the ripples will disappear
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