Visa runs and residency

"He was told" and "I was told" are really common in Central America. When I first moved to Costa Rica I tended to believe most of those stories. 12+ years later, I tend not to.
What type of residency you are talking about may matter but, having done residency in Costa Rica and Nicaragua, at least pensionado residency here (not what I did in CR and Nicaragua) is pretty close to automatic. Things here seem to happen as described and on time.
As for the "visa reset", I have never heard of getting an extension and I know quite a few people who wish it existed. That said, as I learned in Costa Rica, it is "your passport" that needs to leave the country -- the common abuse of the reset seems to cost from $50 to $100 here. I did this in Nicaragua ($20) but actually had residency here before I moved here.

I live in Guat. I have my permanent residency (retired. called rentista)
There is NO "automatic" residency here. You can continue doing the run every 90 days unless they change the law. You will still be a 'tourist'.
The other post is correct - the passport what must make the run. My friend has sent his passport with a trusted person to get it stamped to keep it current.
There is a 90day extension available to the 90day tourist visa. It does cost, and you must begin the process at least several (don't know exact number) days before it expires.

I highly recommend Bety Lopez ([email protected], 502 2360-0156, 502 5428-4468) for assistance with residency issues. She is a 'tramitador', which is a person who specializes in getting residency. You do NOT need an attorney. She has those available when needed. She will instruct you on everything you will need. Believe me, it is quite a lot, and the process is quite involved (Every document must be notarized, then sent to Secretary of State to 'certify' the notary, then to correct Guatemalan Consulate to be 'authenticated', and all this BEFORE you come to apply. And the 'no criminal' report must be less than 6 months old when apply.) Did it all, and got residency in just under 6 months.

Has anyone been questioned at the Guate or Mexican airport or border about entry/exit stamps in their passport? Because they don't appear in the computer system?
After 14 years of visa runs, extensions, and using local services to take my passport to the Mexican border, I recently ran into a little snag. When leaving Guate via the airport, the migration scanned my passport and perused the pages to collate the existing stamps with what's on the computer system. She noticed Guate exit and entry stamps that weren't on the computer and promptly asked me where I went and for how long. I just played dumb, offered no explanation, she gave up and just stamped my passport with her exit stamp and I caught my flight.
This got me worried and looking further into it, apparently all exits and entries need to be in the computer system, airport or border. Also happening in Mexico. I have heard of people being stopped at the Mexican border, hassled and refused entry.
To avoid further problems, I renewed my passport.

While this has never happened to me, it isn't a surprise. When I applied for Nicaraguan residency I had to get a "movamientos migratorios" document and was surprised to see it contained all my entries and exits including a one-day visit from half a dozen years earlier.

My passport did have one or two entries where it traveled to Honduras and back (without me) but, in every case, I know the data was entered into the computer system.

Thanks for the response.
On a side note, had you heard about the old mayor of San Marcos, Don Salvador? The government did an audit and wanted to see proper receipts for everything he claimed as mayor. He had to sell his properties and cars that he accumulated over the years in office. I think the government is trying to crack down on corruption.