I love that you shared all of this detail about your experience.My first deal was also a house hack (I started a little later than you, I was 25).

I used the line of credit to pay cash for the property, then four months later I sold it.

Did the tenant(s) ever receive any legal notices (late rent, noise, unauthorized occupants, notice to vacate, etc.)?

Fast forward twenty years and (maybe a $100M in cumulative real estate transactions later) and I'm still advising investors on asset management, typically focused on real estate as an agent OR mortgage broker, but conversely with clientele of my own age group with similar goals. 

For example, dealing with late rent, property damage, or antisocial behavior can take its toll physically, mentally, and emotionally.

It's caught up now. 20 years later.

Do you find that this process pays off in terms of fewer headaches or challenges later in the project?

The implications of taking money from a retirement account(if not Roth) is that the distribution will be considered income and potentially subject to a 10% penalty.In my opinion, real estate investments and securities within a retirement account are used towards your later years.So it doesn't matter whether it is in one bucket or the other.If you are subject to the 10% penalty, I would only take out a distribution if you strongly beleive your return from real estate will be several percentage points higher than what you can invest in with your IRA.For example, if your return within the IRA is about 8% and you can make 10% in real estate, I would consider doing the distribution because the extra return will pay off the penalty over a few years.Best of luck

In my own experience, when a tenant needs 2 jobs (not 2 people have 1 job each) just to make rent standards will ensure frequent repeated late rent payments.Consistent long paying jobs and income history is more indicative of stable rent collections.Keep looking.  

He was born in kidney failure and later we discovered he has liver cancer.