Paris,
25-30% deposit is standard for upgrades. No getting around it.
In terms of what to upgrade with the builder and what to do with an outside contractor after COE, the rule of thumb is anything structural, electrical or plumbing should be done with the builder. For example, conservatory, fireplaces, recessed lighting, bifold doors, hose bibs, extra outlets and low voltage wiring should be done with the builder. Other options are personal preference and depends on your cash availability and time after COE. Some are easy after COE like crown moldings and painting, others are bit more challenging. I always caution ppl on flooring after COE as even tho it's always cheaper, sometimes it's a royal PIA especially if you're planning on moving in right after you get keys. The aftermarket flooring CO will have to move out the big ass range, unbolt and re bolt the built in fridge and remove & replace the toilets. Flooring companies do this all the time and usually everything is fine. But in rare circumstances, there can be a water leak and going with an outside flooring company will void your plumbing warranty from the builder. And something ppl never think about is the stairs. Say you want all wood stairs but got standard carpeting on it from the builder, it's very difficult and cost prohibitive to change the treads after COE once the newels and balusters are in place, in fact basically logistically impossible, unless you wanted to change your whole stair system. Just food for thought. Cabinetry, I would go with the builder. One thing I always recommend is added insulation. I think it's a must. Good luck and enjoy the process. It's exciting.