Hello and welcome to forum.
I am also mainly using kindle to read research papers. PDF files with two columns are running smoothly and fast on kindle (from the performance point of view). The problem is that, in 100% zoom level, the text is very small and somehow impossible to read. (If you want to simulate the real size of text on 100% zoom level in kindle, try to zoom out the PDF in your PC screen until it is approximately 6 inches.)
Possible solutions:
Don't forget you can make pinch and zoom to make text bigger. Zoom levels are predefined and you need to use your finder to navigate manually.
View the pdf in vertical(landscape) mode. Now the text is almost twice big and easy to read and navigate.
If you can view the full article in your browser, then you can use amazon extension, namely send to Chrome. Now you can read the text and have any deliberate zoom level. The only downside is Latex math formulas are not appearing sometimes.
Almost all academic papers are written in Latex format. You can convert the PDF to Latex then modify it to have better zoom level or even change the number of columns for kindle and then convert it back to PDF and finally send it to Kindle. For similar solutions and approaches, take a look here.
You can use wide range of other devices available with additional functionalities. I suggest to take a look at this great review.
If you can jailbreak the kindle, then you can use any sort of viewer.
Finally, if you want, send me an example and I can test it in my kindle.