2 gerunds in past tense

It is grammatically correct, and it definitely does not sound "weird" to native speakers. It sounds normal. It is the right verb form to use if you are focusing on the time that two actions were taking place together. Jim, while walking to work, was thinking about lunch. Mary, while watching TV, was eating a pizza.

Also, if the shoes were on Ben's own feet, you would write (and say):

Ben, while taking off his shoes, was thinking, "something"

Your examples sound natural to me, it might be because of the use of quotation marks, as the sentence, here as a dialog tag, suddenly gets cut off. But if you say it's correct, that puts me on ease.
Also thank you for correcting that mistake. I'm afraid I make them notoriously and just can't stop.

Krop, if he'sd saying it to himself,

"something, something...."

Nono, I wrote anything just to fill the space for the sake of showing that the sentence is a dialog tag, if that could have any connotations.

Pay no attention to dale, he's an attention seeker who deliberately gives misleading and wrong advice to English leaners. Centrox knows what he's talking about, he won't lead you astray.

Aha !!

Alas Iz, must be very hard to do

It is, most of these people are newcomers and are unaware of your nasty little habits.

Puts you at ease.

Here is perhaps a better example:

Ben, while taking off his shoes, was thinking, "I need some new shoes."

Alas Iz I regularly post an OP warning 'em