A. Have each guild leader make a new free guild and grant them a free ship of equal stature to the one they have currently. Or the free astral whatevers to acquire it. This shouldn't be hard.
B. Existing renown. Snapshot the total at the final moment, plug in those numbers into the code. Or if that's too simple, create a couple guild renown clickies similar to xp grant clickies that equal the guild renoun level and pop them into the guild leader's inventory to 'claim'. Or go the XP stone route except for guild renoun. Shouldn't ultimately be hard, whichever way.
C. Amenities: Once again. The game knows what amenities are on each ship. Should be an easy grant to plop them into the guild leader's inventory, if not automatically, then manually from a DM POV.
D. Guild Chest Contents. After all this is settled, have each guild leader make an alt/series of alts (or if no space is available, an alt acct and then an alt/series of alts there) to collect and mule all the items over to the new server/ship as free transfers. This assumes character transfers have been cleanly established already.
E. Individual Renown contribution. Let's face it, the only thing this does is penalize the guild when someone leaves. This could literally be set to zero to the guild's benefit and no one's loss.
F. Delinquent Guild Members. Assuming the old guild is being abandoned for the new one. Assuming the old guild still exists in some way or another until the termination of the origin server (should that be in the cards). Then they (the delinquent returning guild member) can figure things out when they log back in. They should be able to remember or identify what guild they are in and reach out to the new guild on the new server. Have the guild leader put the new server info in the abandoned message of the day if there are more than one new servers.
G. Ship Names? I didn't realize the ships had names. Hah. Free name change credit? I can't imagine they have to be unique.
This is just a quick take.