Using Multiple Choice for longitudinal surveys

This depends on the type of data you are requesting from the respondent. If you scroll down in that guide, you can easily set the default choices in the subsequent surveys based on embedded data fields that are set in the contact list described also in the guide. You should not need JS for for just setting the default value, for example, of a respondent's selected country using this method.

The default choices only work in text entry for the subsequent survey. I would like to retain the multiple choice option

So, try using the recode values of the multiple choice selections to set the default values for the subsequent survey questions.

For multiple choice questions, the only options for default values are the various choices. There is no ability to use any other values.

I was thinking that you could look at two strategies for accomplishing this. One would be to pass the information via query strings. Since you are already sending the login id as a query parameters, you could also look at sending the MC answers.
Another option could be to store these MC choices in an embedded data, update its value through the contact field and only display the question from the second survey onwards if people want to update their answer. For example, Define an embedded variable gender, which is to be filled via the contact directory. In the first survey, this field will be empty. You use display logic to only show the gender question if the embedded variable gender is empty. So, the question is visible in the first survey, but from the second survey onwards it won't be.