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I have secured floor boards and laid 15mm exterior ply, screwed at every 6ins and a few extras, there are a couple joins that don't line up exactly along the whole length of the board by approx 1mm.
Do I need to lift the boards and try to get them to line up exactly?
Then what is the next steps before laying the tiles

No need to lift and do again.

Next step is to prime with a suitable primer which is recommended by the adhesive manufacturer you are using.

Thanks once again ROC,
Hopefully last questions on flooring,
All holes were drilled and countersunk before putting in screws, do they need to be filled or treated before tiling, and I am going to fit the units and tile up to the feet, do I need to treat the wood that is not going to be tiled any differently.

No to both question