1.1) We need to be careful here what type of "exogeneity" we have in mind. In the dynamic panel data literature, exogeneity typically refers to the stochastic relationship between the respective variables and the idiosyncratic error component. Thus, we typically call a variable "strictly exogenous" if it is uncorrelated with the idiosyncratic error component for all time periods, even though it might be correlated with the unobserved group-specific error component (aka "fixed effects"). Strictly speaking, the latter correlation still turns those variables endogenous in the classical sense. Now, when it comes to time-invariant regressors, they may or may not be correlated with either of the error components, although typically we would assume it to be uncorrelated with the idiosyncratic time-varying error component. In this regard, time-invariant regressors would be strictly exogenous in the dynamic panel data sense, but this is not of much help because we cannot use the typical instruments (lagged differences for levels or lagged levels for differences), because the differences of time-invariant regressors vanish.
1.2) The question whether a dummy variable is exogenous or not is no different to the same question for any other regressor. It may be exogenous, predetermined, or endogenous. It may be correlated with the group-specific effects or not.
1.3) Dummy variables are often treated as exogenous, but this should not be an automatism. Whether you can treat a dummy variable as uncorrelated with the group-specific effects typically depends on what unobserved characteristics you think those group-specific effects represent. Considering time dummies, there is usually no reason not to treat them as exogenous; but we would not give them any structural interpretation anyway.
2.1) Without the factor-variable prefix i., you would include a linear time trend instead of separate time dummies for every year. This would be fine if there is such a linear trend in the time effects indeed.
2.2) If you use i. for the regressors, you should also use i. for the instruments.
2.3) Time dummies are usually treated as exogenous.
3.1) For a binary dummy variable which takes only values 1 or 0, the i. prefix is optional. The results will be the same with or without the prefix.
3.2) See above.
3.3) This depends on what you think the unobserved group-specific error component represents and whether you want to give the country dummy a structural interpretation. If these should be a Japan-specific effect conditional on some other unobserved time-invariant characteristic which differs systematically across countries, then you need to find an alternative instrument which also differs systematically across countries but is uncorrelated with the unobserved characteristic you want to hold fixed. Normally, you would not care too much about such a structural interpretation, and then can just treat the country dummy as exogenous.
4) You don't normally have to include lags of those dummies. Normally, those lags would be dropped because of collinearity anyway.
5) Same as in 4).
6.1) Time dummies are often included to account for global shocks which affect all firms simultaneously. If a global shock affects both the dependent and the independent variables, then omitting the time dummies could lead to spuriously significant coefficient estimates.
6.2) You would include i.cf in the list of independent variables, together with option iv(i.cf).
6.3) Including both cf and i.cf leads to a problem of perfect collinearity. There is no need (and usually no reason) to include cf once you included i.cf (or teffects).
7.1) You need to include the "yes" or "no" manually in the tables of your research paper. The command is not producing anything like that. If you have included time dummies (i.cf or option teffects), you can write "yes"; similarly for country dummies. People still write "yes" even if those dummies are not statistically significant. It is usually just an indication that those dummies are included in the model.
7.2) Whether there are time effects or country effects could be assessed by checking their (joint) statistical significance; but again, the "yes"/"no" in 7.1) is typically not based on such a test.
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