What is the best way to set up an economy for Japan? The trait combo of Aggressive and protectives leaves little in the way of economic bonuses. There are several leaders with such military heavy trait combos.
Is it best to just go with a standard cottage econ although it will be slow? SE if the terrain is right? I have a feeling the best thing for these type of leaders is to play it by ear based on the type of land you start with. Still some guidelines would be helpful. Or perhaps aiming for a couple early Econ-Wonders?

You have to play to the map with Japan and be careful expanding. Japan is slow-but-steady expansion. Don't go crazy pre-medieval--that's the biggest period of weakness for Japan. Expand once during the age of the samurai then wait until gunpowder/drafting. That is where Japan really shines: drafted gunpowder units from rifling onward. Once you hit that point your empire should be uber-workshop heavy (state property, caste system, etc. etc.) and you should be in full-time warfare mostly for the rest of the game until you secure domination.

The same as you would any military civ - by going to war but not keeping the cities.

Give some thought to a moderate Hammer Economy -- high production cities building wealth, research, or troops as needed.

Toku drafting is awesome CI+CGI+DI+Pinch out of a draft. That's a hell of a defender.

Toku's one "hidden" economic bonus is the ability to research pottery from the 1st turn. Fishing can substitute for farming in this regard. ;)

Unfortunately this is a rather situational opportunity. However, if you have grassland river or floodplain in your initial city's bfc, the quick start on cottage growth can give the Japanese economy a much needed boost it wouldn't otherwise enjoy.

A commitment to developing coastal cities can be rewarding as well. Seek out potential city sites that share at least 1 or 2 seafood resources and a couple of decent inland hammer tiles and you are on your way. Coastal tiles don't need to be improved and are fairly productive. This speed enables you to seriously focus on your military goals early on to the near exclusion of other techs. Fishing lets you research sailing early as well, positioning you for the economic benefits of the Great Lighthouse.

As the Japanese you typically work your way down the mining/metals path earlier than some. This can also set you up for the Colossus.

So anyway, the Japanese economy doesn't necessarily need to be a wasteland. Early cottages or coastal tiles + lighthouse/statue & settling the subsequent merchant = bankroll for your early warmongering.

Yea I've often thought the GL is a nice save for civ's like Japan. However I'm trying to getaway from this habit. However maybe it's a necessary choice in this case. The fishing tech dose help with this.

Yes the Samurai do support good conquest, but I was surprised you said to only aim for conquering one civ with them. The only game I played as Japan I used 2 GM to generate enough gold to upgrade 20 pre-build swordsman->samurai. The army dominated.

I hadn't thought of the early access to cottages. This is a definite possibility, although I admit I don't like cottages and try to avoid them if I can. The Hammer Economy I have been experimenting with recently. Although I was using an All-In approach running 0% science slider and building the science instead of using the slider and building wealth. This Wealth option would work better for Japan.

I like the idea of focusing on a coastal economy. An early metalcasting for the Colossus as well would be a huge boost. What do you think about Oricaling it? Priesthood is a little out of the way but Orical ->MC would guaranty the Colossus and give early access to Forges and Workshops, both good for Japan, as well as Triremes I guess. Would this detour be worth it?

Not much different from other aggressive civs, conquer early when it's easiest, axes is better than samurais for this imo though if your economy can take it when you get the latter go for it.
I haven't personally tried chopwhiprushing walls, but maybe there's some good money in that.

I like the idea of focusing on a coastal economy. An early metalcasting for the Colossus as well would be a huge boost. What do you think about Oricaling it? Priesthood is a little out of the way but Orical ->MC would guaranty the Colossus and give early access to Forges and Workshops, both good for Japan, as well as Triremes I guess. Would this detour be worth it?

For my personal playstyle, I'd skip the Oracle for a number of reasons.

I'm reluctant to research those techs when I'm probably not going to receive the religion along with it, plus I'd prefer not to pollute the great people pool with prophets. In my experience the predictable engineer and merchant points are preferable for Japan when using the approach we are discussing.

The economic "bonuses" we are pursuing here are flimsy at best, after all, and their benefit for Japan lies primarily in the speed with which we are applying them. Therefore any deviation from the goals, such as they are, weakens the strategy. YMMV though. :)

If you commit to chasing GL and/or Colossus early, more often than not you'll get em. Place your coastal cities advantageously and they are all but yours. The combined effect of super early seafood resources, metals, slavery, and chopping make it very difficult for foes to beat you to the punch. If you start to feel nervous just whip the remaining hammers out, population be damned -- your seafood resources will grow your city back quickly! Roosevelt and (to a lesser extent) Ragnar seem to be the only real competitors. I've rarely lost out to anyone else.

I'd just use the Oracle path beakers to research metal casting myself. The AI values MC highly and it's great trade material once you've already built the statue.

One last thing is early mining/fishing leaves you poised to benefit from any gems/gold/silver that can still be reached from a coastal city location. That's no revelation in and of itself of course, as those tiles are always coveted, but once again it's the speed with which we are getting them rolling that is the difference. If you can manage such a city (and you often will,) it really takes a lot of the bite out of researching Metal Casting on your own.

Hope you'll let us know how it works out for you if you give it a try. :)

japan is quite weak on the begining (but indestructible. protective archer + aggresive axe), but then got the incredible period :
UU -> overpowered rifles -> UB

its UB gives a 10% production bonus + a strange 'sort of' health bonus since you may decide not to use coal and save 2 unhealthyness from the factory (and allow plant in the NP city :) ).

I'd rather go on a SE/HE with japan (no cotages but in capital), to maintain correct economy until samourais, then prod/draft units like a mad until theres nothing else to conquer and finally go whether for space or domination using the 10% prod bonus.