Alarm bells have started ringing but I'd like some pro advice if I'm on the right track.

Or is this a lender that you have an established track-record with?

If I could tell my 19 year old self anything, I'd say your on the right track keep doing what your doing career wise and pat myself on the back.

They must keep track of all invoices to be charged towards the security deposit outside the scope of normal wear and tear.

I wish I knew this 10 years ago and tracked all this better. 

Some lenders will look at your track record, which under a new LLC will be zero (which could be your problem).

Submit maintenance and track through to completion.

Track each and every penny in detail in your accounting software any time you make a payment, and there you have a list ready at the end of the year with date, amount, vendor, and type of expense. 

WHICH ones do you like, that have communications Built-in, through an APIs, and can track response of marketing outreach programs like text messages?

Don’t just pick the cheapest bid get someone who will do quality work and has a good track record.