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Recently i have been doing some minor conversions turning chaos space marines into space skaven to make a nurgle army lists. I've been wondering though using the gift of mutation but in keeping with my army I would try to use a rat orge as a chaos spawn and a Vermin lord as a daemon prince and just covering them with copious amounts of green stuff to make them look more mutated/plaguey. and i was wondering if this would be ok as long hey were on appropriate sized round bases.

That is a question for your opponents or your TO as there is no hard rule about conversions or scratch builds being legal or not.

I use Dire Wolves with some extra bits as spawn in my army and no one has had a problem with them.

As long as they are about the same size and fit the theme of your army, most people don't care about the actual models being used.

Vermin Lord might be a bit small for a daemon prince though. There was a conversion of a daemon prince model into a vermin lord I saw a while back which looked very cool.

as CrownAxe points out:
It is your opponents permission you need, not some voiceless faceless entities on the internet whom are more then willing to accept proxies. There are no Rules at all relating to how to go about using Proxies, therefore the only way to use one in the game would require adding a few sentences to the Rulebook allowing permission to use Proxies. Given that this involves altering the Rulebook, and such alterations can only occur via Opponent Agreement, it is now required by the Written Rules that you go out and talk to your opponent about this matter.

Does anybody know what the base size for a Fantasy Vermin lord is, I have a suspicion its 40mm. If so I can get a nurgle deamon lord and attempt to ram the two together.

50mm Monster base.

I use converted rat ogres and have never had a problem

I'm another chaos spawn = rat ogre user, and no issues here.
As previously mentioned bring it up with your opponent first. If they have a problem with you using models in-theme with the rest of your army, you really didn't want to waste time playing against them in the first place.