I don't think you will have any problems leaving the forks compressed for several days. The seals are not really under pressure when compressed, the springs are, but there shouldn't be much if any pressure on the seals. I just noticed you have air forks, but I still don't think you will have any problems.
I would compress the front end at least half way for transport. Use tiedown points as close to the triple tree as you can. The bars may bend if subjected to a big pothole, and the bike bounced. I would also use the upper shock mounting area for the rear tiedown. The higher you can attach to, the better. Also compress the rear end half way to keep it from sliding. As an extra precaution, if you have a wood bed on the trailer is to screw down a couple of two by fours along side the tires, front to back. Or short blocks on either side of the wheels would work too. There is a tendency for the tires to want to slide out from under the bike on bad roads.
I would not use the center stand or the side stand. These cannot absorb any shocks and can either bend the stands, or bend the frame. As to leaving it in gear, I probably wouldn't. You don't want the transmission or clutch to be constantly under back and forth pressure. Try to tie the front wheel to the front of the trailer and you shouldn't need to have it in gear. Check the tautness of the tiedowns at gas stops and after the first 20 miles or so. They will tend to stretch a bit at first.