Aye Richard,
Will it matter if there is some paraffin traces left in the oil tank and gearbox?
So long as there are not puddles, it will probably be OK. Getting rid of the paraffin using the brake cleaner, is my way of doing it, as the brake cleaner evaporates after the sluicing.
Is there any reason not to use the semi synthetic I normally run the bike on for the first run?
None whatsoever, if that is all that you have and the bike doesn't require "running in"? It's because of the additives in the semi-synthetic oil provide such good lubrication that they can hinder the "running in" bedding in process of new components.
...... so will it be ok just running it on the stand till it is good and hot or will that not do the job?
Taking the bike out for a wee canter, will ensure that the oil gets sloshed about on all the bearing/contact surfaces, sitting on the centre stand may not be as effective. However, if you warm the engine through gently to start off and once up to temperature increase the throttle up to 4K to 5K, it will be better than doing nothing. Some might say it is a bit of overkill, but I think the wee canter near to home helps you familiarise yourself with the bike, you find any wee leaks or "strange noises", without being too far from home and you can dump the oil whilst everything is hot, all in one go. Nothing worse than finding a leak or weep, with the running oil in the tank and you have to drain it all off to cure the leak.
As a final tip, rather than paying silly money for branded oils try either 'Westway' [
Westway_Oils_link], they sell direct or via eBay, or 'Smith+Allan' [
'Smith+Allan'_link], who sell direct. Both produce good oils at very reasonable prices, IMHO, delivered to your door. On Friday last I ordered 20litres of oil from 'Smith+Allan' just before 14:00hrs and it was delivered this Monday morning to my door before 11:00hrs. All for under £75-00, whereas the Silkolene (Fuchs) equivilent, is just shy of £200-00 for the same quantity.

Keep us posted.
Good health, Bill