More great stuff, Mr.G!
As for the 'X' symbol for X-Gerat, it's a difficult one, and some of the decision would depend on the period in the aircraft's life that you wish to ultimately display it. If, for instance, you wish to display the restored aircraft as it was during the BoB, and the original fuselage 'X' was then yellow, then that is the colour ir should be. You will know more, but I suspect that the colour change was made after moving to Norway, i.e. after the BoB.
As for the tail 'X', if you have evidence that it was present, then yes, it should be re-painted. But, would the aircraft carry TWO 'X' symbols?
It may be that, during the BoB, the tail was the 'standard' place to put the 'X', and that it moved later, which I know contradicts what I have said above. As there is definite proof of the 'X' being on the fuselage, then obviously this should be re-painted, as for the tail, as Erich said, probably yes, but it will be down to your 'gut' feeling, or further research/evidence.
In conclusion, I would think that, a restored Authentic JU88A1, with a combat history, would not look out of place with both markings, and there is evidence of other matkings, such as 'group leader' bars, being duplicated on wings and tail on He111's.
Jan, re the best kit in 1/48th for your JU88A1/A5 conversion. I would guess that those available, Revell/Dragon, MIGHT be best, but I've only seen photos. The old Hobbycraft one that I used is accurate in general outline, the thing that lets it down is the 'heavy' appearance of the transparencies. However, you would need to mould at least a new rear canopy top section, and I still have the mould I made for mine. Also, the engine nacelles need modifying, which is fairly simple with a bit of surgery and 'Milliput' rather than going to the expense of a convesion kit. For the A1, the outer wing needs re-shaping and shortening, and this is shown on the plans I have. The rest I'm sure you can glean from all the info Mr.G has posted, or has on his web-site. If you need plans or other stuff, let me know.
Terry.