Filing the I-130 is not an issue. There is no bar on filing a family based immigration petition.
Filing the I-485 could be an issue depending on what CBP asked and what she told CBP about her intent to adjust status.
You being a public charge will require a well qualified joint sponsor, and that is about it.
She will need work authorization, EAD, to work. This can take up to 8 months to process.
You cannot "apply in person". I-130 is filed by you. I-485 is filed by your wife (along with I-765 and I-131), and I-864 by you and another I-864 by her joint sponsor. There is a fee waiver form, but it's based on certain specifics, like asylum or country specific Acts. More information here:
https://www.uscis.gov/i-912
I don't know of any lawyer that would take this case for less than $thousand(s). There are community resources from churches and such, but they mostly help with asylum and similar cases.
You can file anytime. The risk is if you file after her I-94 expires, she can be deported or held in immigration enforcement at anytime (there was a poster who was jailed after a traffic accident when police checked her status - she was only a week or so "late" in filing the I-485 and was planning to do so that week).