Managed to get it sorted.... ended up removing the glove box & was able to move the fan into the correct position. See picture of how far out of alignment I was.. I don't think it would have mattered how many times I'd tried to aligned it from underneath it was never going to go in.

It's bitter sweet anyway as now when I run the fan at full speed it vibrates badly, think I've damaged one of the blades on the fan... time to find a replacement..