1 month in Japan

Hello everybody!
I was lucky enough to be accepted for a 3 weeks-long (from the 1st to the 19th of August) clerkship in Osaka for August.
I've never been to Japan before, so I really hope to see as much as possible of the country.
I'll be busy working from mondays to fridays till 5pm, therefore I'll be travelling only on the weekends at least for the first 3 weeks. For this reason, I was planning of visiting everything close to Osaka during that period and moving to Tokyo for the last 12-13 days (I'm going back on the 4th of september).
Based heavely on the suggested itineraries on this site, I was thinking to something like this as a schedule:
- 1st weekend (6th-7th aug): Kyoto
Eastern Kyoto Full Day
Arashiyama Full Day

- 2nd weekend (13th-14th aug)
Mount Koya
Nara

-End of clerkship (I'm free!)

-20th aug
Kobe (is it worth it?)

-21st aug
Northern Kyoto Half Day

-22nd-24th aug
[empty slot]

-25th aug: I'm probably buying a 7d Japan Rail Pass
Hiroshima-Miyiajima (sleep there)

-26th aug -1st Sept (each line is a day)
-Himeji and travel to Tokyo (sleep there)
-Western Tokyo Full day
-Asakusa and Odaiba Full day
-Imperial Palace and Ginza half day
-Kamakura
-Nikko
-Takayama

-2nd-3rd sept
[empty slot]

-4th of sept. going back home!

So, this was the general plan, as you can see there are a couple of empty slots, any idea on how to fill them?
What do you guys think about it? Is there any improvement that can be made? I'm 100% open to suggestions of any kind.
Thanks for everything!

P.S. I'll be taking the flight back from Tokyo Narita
P.P.S. For the first 3 weeks I'd like to sleep in Osaka whenever possible, as an accomodation has been provided to me.

Put Nara on a different weekend to Koyasan.

Considering Takayama's location. That should be done on the way to Tokyo. Not a day trip from Tokyo.

- 1st weekend (6th-7th aug): Kyoto
Eastern Kyoto Full Day
Arashiyama Full Day
- 2nd weekend (13th-14th aug)
Mount Koya
Nara

I think it is good.

-End of clerkship (I'm free!)

-20th aug
Kobe (is it worth it?)

You can do Kobe as a night out from Osaka. Any Monday to Friday. It is a city with night life like Osaka and the night view atop Mt Rokko is nice. Don't have to use a day for this. Perhaps instead visit Okayama on this 20th.

-21st aug
Northern Kyoto Half Day

-22nd-24th aug
[empty slot]

I would rather spend days 21 to 24 in Kyoto if you have the time. don't have to go back and forth between Kyoto and Osaka. Perhaps a visit to an onsen town near Osaka or to Ise/Uji on the first weekend?

Four days for the four directions.
North, South, East, and West. Since South has little, you can do central too on that day.

-25th aug: I'm probably buying a 7d Japan Rail Pass
Hiroshima-Miyiajima (sleep there)

-26th aug -1st Sept (each line is a day)
-Himeji and travel to Tokyo (sleep there)
-Western Tokyo Full day
-Asakusa and Odaiba Full day
-Imperial Palace and Ginza half day
-Kamakura
-Nikko
-Takayama

What do you mean by Western Tokyo?
Takayama is too far to do from a trip from Tokyo.
Instead you may want to use your first weekend to take the train from Osaka to Kanazawa/Takayama and back again.

-2nd-3rd sept
[empty slot]

There is always Fuji 5 lakes and Hakone.

First of all, thanks to both for the help!
So, i tried to rearrange everything according to the suggestions and here's what I got:

- 1st weekend (6th-7th aug)
Ise
Nara
- 2nd weekend (13th-14th aug)
Mount Koya
[empty slot]
-End of clerkship (I'm free!)
-20th aug
Eastern Kyoto Full Day

-21st aug
Arashiyama (Western kyoto) Full Day
-22nd aug
Northern Kyoto Half Day
-23th aug
Southern Kyoto + Central Kyoto
Unfortunately I�fll have to go back and forth between Osaka and Kyoto�c Having an accommodation in Osaka will save me a lot of money.
-24th aug: I'm probably buying a 7d Japan Rail Pass
Okayama (sleep there)
-25th aug:
Hiroshima-Miyiajima (sleep there)
-26th aug:
Himeji and travel to Takayama (sleep there)

-27th aug (sleeping in Tokyo from now on)
Visit Takayama and travel to Tokyo
-28th aug
Western Tokyo (there�fs a suggested itinerary called �gwestern Tokyo full day�h it includes meji shrine, takeshita dori, omotesando, shibuya, Shinjuku)

29th aug-2nd sept (each line is a day)
Asakusa and Odaiba Full day
Kamakura
Imperial Palace and Ginza Half Day
Nikko

-3rd sept
[empty slot]: I�fll probably spend the last day doing some shopping in Tokyo :D
-4th of sept. going back home!

Sounds pretty solid to me.. Right? :P

Hiroshima needs a full day and so does Miyajima. Please try to find another day in your schedule to do this, or drop Okayama unless there is something uber important for picking Okayama.

so, you'd suggest something like this, right?
-24th aug: I'm probably buying a 7d Japan Rail Pass
Hiroshima (sleep there)

-25th aug:
Miyiajima (sleep there)

That would work. would be much cheaper just to have a hotel in Hiroshima for the 2 nights. But up to you.

JR Nation Wide Rail Passes have to be purchased outside Japan. Have you allowed yourself enough time for the exchange order to be sent to you or to get to an approved reseller to purchase?

absolutely not O.O
But I'll be needing it starting from the 25th... am I still in time? Do they deliver it to Japanese adresses?

Ok! I should have someone sending it to me while I'm there.

Thanks again for all the help guys

When you say "clerkship" do you still enter on a tourist visa? Because I think you're passport has to be stamped tourist visa entry to use JR pass- I"m sure someone will correct me if I'm wrong?

I disagree that Hiroshima and Miyajima needs two days and not one. It depends on the person. E.g. is going to a car museum (Mazda) or visiting a castle in your list (Himeji and Osaka has better ones) & how fast said person can move from location to location.

yeah that is right... i already know that and actually I'm not 100% sure on what I'm going to say yet. I mean... it's a clerkship, I'm not gonna be paid, it's not like I'll be working there. The best definition I could give about my situation is "visiting student", would I be eligible for the JR pass?
What should I do?

when entering the country, what are you telling them you are in the country for? Have you applied for a visa?

Unpaid clerkships of less than 90 days can be done on a visa waiver. Plus since you don't already have a work visa or similar in hand, then this is probably the route that the program expects you to take. Contact them to be sure.

A few comments on your itinerary:

Koyasan is best done over the entire weekend. I'd suggest staying overnight at temple and visiting Okunoin at night.

Okayama is a pretty boring place to stay. There's stuff to see during the day (have anything specific in mind yet?), but you could stay somewhere else in the evening.

Hiroshima/Miyajima can be done in a day. I've done it before. I'm a really fast traveller, but still that limits you to pretty much just the Peace Park and the lower parts of Miyajima and it will be rushed. 2 days is better if you can spare them.

I suppose for your Tokyo time you are planning to do the itineraries listed on this site? That's a lot of travel in a row. Not sure how well you travel for long periods, but don't be afraid to schedule in a rest day. Maybe put your shopping day in the middle of the walking tours so you don't get burned out.

You were right, i talked to the org and a tourist visa is fine (i went in full panic mode for a couple of minutes) :D

Regarding the corrections on the itinerary, i decided to drop completely Okayama, and I'll be spending the entire weekend on Koyasan as you suggested (is there any cheap solution for spending the night there? :P).