Searching for articles published in Japan can be challenging, and involve the use of multiple databases. Moreover, it is difficult to find journals with electronic access. However, more and more university and research group publications are coming online as open access resources, and it's possible to obtain more research that is freely available online. Other databases can direct you to where to find articles in print, both historical sources and contemporary research.
These databases do not provide full text for every article citation, but do so for the majority. Articles are provided through institutional repositories as well as other databases.
To limit your search to only downloadable articles, check the option 本文あり near the search bar.
If Penn owns the journal or book you need a PDF from, there's no need to photocopy it yourself. From the item's Franklin page, log in to your account and click "Scan & Deliver." Fill out the form in roman characters with no diacritics and be sure to supply as much information as you can (especially journal title and year/issue/page numbers) so library staff who do not read Japanese can find your article. It will be delivered to you as a PDF.
You can get articles in print journals held by other libraries in North America and NDL using Inter Library Loan (ILL). To order articles through ILL, go to Penn Libraries' Document Delivery homepage. They will be scanned and delivered to you as a PDF. Simply request Japanese articles using the ILL form, entering it in roman characters with no diacritics in the form, and note in the comment box "National Diet Library of Japan" if it's only held by NDL. (You can check in WorldCat to see whether the journal is available in North America or only in Japan.)
MagazinePlus has the ability to browse journals, look at the most recent article citations posted, and also aggregate the detailed views of your search results into one window that can be exported into a file. To export your citations in TSV, CSV, or BibTex format (the former two being good for Excel, and the latter for citation managers), click on the citations from your results that you want to include in your list. Then click "チェックした文献を詳細表示". This will bring up a new window, where you can click on your preferred file type at the top of the page and export to a file from there. The file will automatically download.
CiNii also lets you bulk download your results in a variety of file formats. From the search result page, check the results you want to export, then next to that you can choose file type from the dropdown. Finally, click 実行 and download the file.
To view the CSV (*.csv) or TSV (*.txt) files in Excel, you must import them with their proper encoding. Open a file (such as a new workbook), then use the "import" function in Excel, under the "file" menu. Click on "import," choose the file type and file, and then make sure to choose "Unicode UTF-8" as the language. If this doesn't work (it will display the text in a preview window) keep checking different types of encodings until you see the Japanese text displayed properly.
Kōseisha Zasshi kiji sakuin shūsei database 皓星社雑誌記事索引集成データベース provides a fairly simple interface for searching, but has some more advanced options as well.
First, go to the advanced search 詳細検索 link. Note that if you enter a space in your keyword string, it will function as a boolean AND (so all words will have to be included in the results - it won't search keyword1 OR keyword 2). To use a thesaurus to broaden your search, check 利用する next to 類語辞典. To integrate a search of CiNii Articles or NDL Digital Collections as well as Kōseisha, check 利用する next to CiNii and/or NDL.
Be aware the Kōseisha database will convert 旧漢字 to modern characters in its search, and also has a list of pseudonyms associated with a person; if a person wrote an article under a lesser-known pseudonym, a search for his or her standard name will still bring up that article. So you can search with confidence knowing that the database will resolve your modern kanji with 旧漢字 and standard names to pseudonyms, without having to specifically enter those versions yourself. However, if you search for a pseudonym, it won't resolve that pseudonym back to the standard name, and entering 当て字 instead of katakana for foreign names will likewise not resolve back to the standard name. (So, enter the standard modern name.)
Additionally, note that searching for a personal name using the basic search will bring up results both by and about that person; to retrieve only results for one or the other, use the advanced search.
Kōseisha graphs your results for you too so that you can see trends over time in publishing about your keywords. It differentiates CiNii and NDL data from Kōseisha index results.