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I know there were 300,000 Ultramarines Pre-Herey and Pre-Calth but how was the Legion organized? I can't seem to find any information on this at all.

Also did Roboute have an Honour Guard?

There were 250,000 marines.

They were divided into 250 chapters. The novel 'Know No Fear' calls these chapters Companies, but that is confusing so we'll call them chapters.
Each chapter is like a modern chapter. The main difference is that each chapter was divided into two "battalions" of 500 each led by a Lord Commander.

Forge World has recently released a book on the Horus Heresy which amongst other things, gives a break down of the average legion.