On the initial level most all rules are fully compatible as FantasyCraft and NarutoD20/D20 Modern use the OGl D20 system.
They both utilize the level based Defense attribute instead of AC, simplifying some of it. The following are the first couple of changes to bring the systems together cohesively.
1.) Action Points vs Action Dice: The Action Dice system will port over to a hybrid much more simply than the Action Point system. This brings some advantage to the NarutoD20 rules, as well.
2.) Replace Reputation and Wealth: The FantasyCraft System of Lifestyle and Legend work out a bit smoother with helping shape characters.
3.) Techniques vs Spells: Personally I feel replacing the spell system completely for the Technique System is marvelous. The magical classes from FantasyCraft fit with the game using a Skill Based Casting system, but the spells themselves may need to be altered. As an alternative, the spell system could be left in intact and represents a different theory of magic, (East meets West)
4.) DRmor: Converting all Armor to Damage Reduction instead of Defense is a personal preference of mine.
5.) Bloodlines and ECL: Bloodlines can be converted from level dips to Human Talents relatively easily, just require feat expenditures on the future level dips beyond first. Moujou Aishou is easily replaced by a better feat Animal Partner, with no level loss.
6.) Occupations and Specialty: I may just be a power glutton, but I feel they go together well to bring a starting character closer to a full blown character.
This opens A LOT of areas for abuse, but I would think the potential problems are outweighed greatly by the potential AWESOME.
The only way to refine it, IMO, is to playtest it and make extensive notes about what does and does not work. With all the digital documentation, a possible Play-By-Post or IRC game may be best... or laptops all around, hah.