I'm very familiar with 3.5, somewhat familiar with PF, but only know the core ruleset of 4e. Nevertheless, since no one else has answered, I thought I might as well take a stab at the major differences. I'd say the general theme is that PF offers more paths while building a character, at the cost of offering more dead ends as well. Similarly, monsters are more flexible, but more difficult for the DM to run.
I think you could write an interesting essay talking more about the philosophical and design differences between the two systems, but in answering this question it'll be more useful to address the observable differences point by point.
Class and monster roles
Fourth edition (4e) has clearly defined class and monster roles. This isn't the case at all in Pathfinder (PF). A fighter in PF might be good at dealing damage (striker) or a great tank (defender) but this will depend entirely on how you build your character. Monsters do not provide an obvious indication of how they should be used; the DM has to examine their abilities and think about what their role should be in battle.
It's very easy to build an ineffective character in PF, as a consequence of the greater flexibility you have in defining your role.
Multiclassing
Since in PF each class defines its own progression, every time a PC gains a level they can choose what class to advance in. Again, this means it is possible to design a character that performs very poorly. It would be a bit like creating a 4e character that drew from multiple classes, but was capable of using only heroic level powers while everyone else was choosing a paragon path.
Paths vs. Prestige Classes
In 4e, there are three distinct tiers of play, and you can choose a paragon path and epic destiny as you progress.
There's no direct analogue to the tiers in PF. The closest thing to a paragon path is a prestige class -- a class that can only be taken when you meet certain requirements. This was more of a big deal in 3.5, where it was used for character customization; in PF there are many fewer prestige classes, though they might be important for certain multiclass combinations.
Defenses v. Saves
This is purely technical, but confusing if you're not expecting it. Defenses in 4e are equivalent to saving throws in PF. If a wizard casts a spell, rather than rolling an attack, the defender rolls a saving throw against a DC set by the spell.
Automatic progressions
In 4e, you add half your level to a great many statistics. PF is not quite so straightforward -- your class(es) will determine your base attack bonus and saving throw progression, and you must pick how your skills improve every level. Other abilities like AC or initiative do not naturally increase as you level.
Powers, Spells, and Maneuvers
This is probably the most fundamental difference from a player's perspective.
In 4e, every class has a list of powers they can learn as they level. These powers are divided into at-will, daily, and encounter powers that dictate how often they can be used. Pretty much any special ability a player has is derived from a power -- and those powers are chiefly geared towards combat. Casting classes can gain rituals which are less combat related, and work off a different economy than combat powers.
In Pathfinder, it works a little differently. Casting classes have spells, which are probably closest in spirit to 4e powers, but tend to be more flexible. The number of spells you can choose from is quite large, and different classes have different mechanics for learning and casting these spells. Spells useful in combat consume exactly the same resources as more role-playing oriented spells.
Meanwhile, melee classes rarely have the same type of limited powers. Anyone can push, grab, pull, grapple, trip or disarm a foe during combat, and you can do so as often as you like. Doing so means sacrificing damage, though; you will only do damage with a regular attack. Unlike 4e, forced movement is quite difficult to pull off in PF, which is why a grid isn't as necessary.
As an example, a fighter in PF progresses chiefly because they get better at what they've been capable of doing all along, rather than getting spectacular new powers.
Monsters
This is a big difference from the DM's POV especially.
In addition to fitting certain roles (as mentioned above) monsters in 4e are often defined by a set of bespoke abilities. In contrast, monsters in PF always play by the same rules as the players. Their hp, attacks, saves, and skills are defined and limited by the type and HD of the monster. The majority of unique special abilities are copies of spells, or one of a small set of abilities common to many monsters. Often a powerful monster will have a large set of abilities they will never use in combat, but can provide role playing hooks.
There is no PF equivalent to elite or solo monsters -- you simply must use a higher level beast to provide a greater challenge to the party.
Overall the 4e system is much easier on the DM in creating encounters. For those so inclined, though, the PF system allows the creation of some interesting beasts; you can even add class levels to monsters, much like PCs can multiclass.
Magic items
The majority of magic items in PF do one of two things -- they either increase the attributes of a PC, or they can replicate the effects of spells. Magic weapons and armor combine several different attributes, almost Diablo style. Compared to the 4e items in core, they are much more varied, and what specific item your character has can drastically affect what they can do. The downside is that it becomes harder for a player to choose the 'correct' gear.
Since I am really involved in D&D 3.0 and 3.5 I can answer your question but you will not like my answer; In-Setting differences between L5R and D&D in general have so many setting differences that you could write a 3 book novel about it.
The big ones: In D&D your gods are different and thus how the world came to be is much different as is the lore behind your setting, In Oriental Adventures you have the world of Faerun all around you and it can influence your campaign in ways that might change it largely outside your theme of "L5R". Since the Oriental Adventures takes part around the territory of Thay and the Great Dales from the Unapproachable East as in most D&D Faerun based worlds.
BUT this is not the case in your campaign because you are choosing to use the Oriental Adventures custom version of the L5R lore in Rokugan, which by default lends directly to L5R The history of Rokugan;
*
Encompassing more than a thousand years. The last forty or so of those
years are of particular interest, since that is the time period
covered by the Legend of the Five Rings card game and novels. This
chapter cannot hope to describe the events of the Clan Wars, the War
Against the Shadow, and the Spirit Wars in any kind of exhaustive
detail. A summary of key events in those years appears here, and each
clan description below gives a current snapshot of the clan, with
details of the most important events leading up to the present.
*Page 207 of the Oriental Adventures book.
As far as I can read their should be no difference in setting between the L5R series and the D&D 3.0 or 3.5 Game you wish to run unless you specifically change something to form fit your game or world. The differences you mention above about people eating meat is simply an observation that can be over ruled by any GM, also the way to the dragon homelands is completely up to you as the GM to build and thus could easily mirror exactly as it dose in L5R.
Best Answer
Birthright is a larger scale system designed for interaction between multiple mature countries. The AD&D 2nd Edition campaign setting is set in the world of Aebrynis on the continent of Cerilia which is ~very~ detailed at the ruling level. The setting has divine magical "bloodlines" from the old (dead) gods that allow the regents to rule Law, Guild, Temple, Source and Province/Land Holdings as a core concept. Domain development is done in turns, a turn is a season of three months and the regent gets one Domain Action per month. You can construct some general high level holdings, conduct trade and war, etc. but the building is abstracted into Holdings. E.g. Increasing a Temple Holding from level 1 to 2 in a province may involve upgrading your existing chapel, or building another one in a neighbouring village, or it may just result in more worshippers at existing structures.
A fully 3.5e'd version of Birthright has been created by the community at birthright.net. These rules are meant to be the primary focus of a campaign with "adventurer level" action as a sideline. So much so that there is a Domain Action specifically for it called "Adventure".
Kingmaker is mostly a specific adventure path with some specific rules about carving a new civilization out of largely-unsettled areas and being sustainable. It has a more micro focus - exploration and then construction down to the building level ("I build an inn this turn!") Also keep in mind these are supplemental rules in an AP; there's 9 pages of kingdom building rules, then more later on mass combat and exploration, but the core is small. The rules have been reprinted in Ultimate Campaign, but not in significantly more detail. They are suitable for settlement building as an adjunct to a normal campaign.