For my own records, but also for help of future overlanders, I thought I might outline my experience (as I recall it) of each border crossing.
Mexico
I crossed into Mexico at Brownsville, Texas, early on a Tuesday. As always, I first checked into immigration, and then in aduana (customs). Mexico requires a deposit of $400 for a motorcycle, plus a non-refundable fee of about $40. I paid the deposit on my credit card. It was refunded three days after checking out of mexico.
Customs finishes with a document and a sticker for the bike's windshield. All in, it took me under 90 minutes to check in. That said, I was there first thing in the morning, so it could be much longer midday.
I checked out of Mexico in Tapachula. Here, you have to complete the aduana first, in a station on the highway before Tapachula. One knows where it is by way of the frantically waving locals with homemade badges who direct you towards the station. I arrived at the town after the closing of the office, so I returned first thing in the morning. It took me less than twenty minutes to check out, and I required no assistance. The official gives you a document certifying exit, and removes the sticker from the windshield. I then travelled the twenty kms to the border station.
Unlike the crossing in, this station was full of touts. Indeed, it was rather fitting that the border post was also encircled by a large group of vultures. Still, it was an easy crossing out. All in, Mexico was a breeze.
Guatemala
Guatemala was similarly buzzing with touts, though their badges appeared marginally less official. Embarrassingly, I was ripped off by money changers here. Having let my guard down, I exchanged money with a man who counted the money is his hand, rather than laying down the bills before me. My four rules of exchanging money:
1. Know the exchange rate and know how much you expect for your money ahead of time.
2. Always insist on money being laid out, bill by bill, in front of you. A bill is only counted sheen it leaves a hand.
3. Hand your own money over only after counting and controlling the new currency.
4. Remember faces.
Guatemala, like Mexico, required a windshield sticker. The total cost was about $15, and was all completed at one window, with the exception of payment, which happens one office over.
When it came time to pay, i was short as a result of the earlier counting scam. So, I left the customs official my title and rode into the nearest town to get money from a cajero.
Customs here were very straightforward, and I required no help. Save the self-imposed time loss, this was less than a one hour process.
I don't recall the exit from Guatemala very well, but I do remember it being rather straightforward.
El Salvador
Entering El Salvador was rather simple. I was stopped on the bridge into the country, and ws made to fill out a form. After doing so, the officer checked my VIN, and then sent me to the aduana office. There, all of my information was entered into a computer by another official. I was given a stamped paper confirming my temporary importation. Following this (contrary to convention), I checked into immigration. Because of an agreement with Guatemala, El Salvador did not stamp my passport. I was then off. The entire process was free. It was slow, but not overly so.
Checking out of El Salvador was unremarkable.
Honduras
Entering Honduras was the sole time in Central America I made use of an agent. I am not sure I needed his help, but I was pressed for time and wanted to make it to Nicaragua before the border closed, and thus acquiesced. Truth to tell, it just seemed like a lot of running back and forth to the photocopy shop. Otherwise, I think it was rather simple. I imagine one could do this without assistance in under 90 minutes. In total, I paid $16 to import the bike, and $10 to the agent.
The highlight of this entry was that the agent asked me for an additional $10 i n exchange for my information being entered "into the system". I asked him what would happen if I wasn't entered into this magical system. He assured me it would cost me $25 to be put into the system on my way out of the country. How they'd know i was ever in it, I didn't ask. I passed on this charge and had no trouble on the way out.
Nicaragua
Bring a book.
This was easily the slowest border I passed. Everything happened within one building, just very slowly. Note that you have to buy insurance here. It costs less than $20. You also have to pay a nominal amount for your stamp.
I left Nicaragua in the dark. It was truly farcical. There are four steps. First, get an exit stamp. This is easy. Second, find the correct police officer for a signature for the bike form. I found him on the edge of the bush, behind a building. I felt bad about interrupting whatever he was beginning or starting, but I was on a timeline. You then need to get a stamp from another police officer. I found this one hanging out in an insurance office. You then go to another building to be stamped out. All told, this was a longish process, but amusing.
Costa Rica
I went through five steps to enter Costa Rica:
1. Stamp in at immigration.
2. Begin paperwork at the aduana.
3. Buy insurance down the road.
4. Compete paper work at the aduana office.
5. Go the other direction up the road to get the bike stamped out.
Leaving Costa Rica on the pan am took less than 30 minutes. I stamped out and then went a few offices over to get my bike stamped out.
Panama
Panama was simple, but a bit slower. I stamped in, and then bought insurance across the street for less than $20. I then stamped in the bike. This took a while, as the official could not find the bike model in the computer. Nonetheless, it was quite simple, and everything happened in a 200 foot radius.
Columbia, Ecuador and Peru
Leaving aside the process of importing the bike by air into Columbia, traversing these borders was an absolute breeze. None took me longer than 30 minutes, and each was completely free. The officials at these posts were model bureaucrats.
General Comments
After two crossings, I adopted a new approach to borders and touts. First, I rode in with my dark windscreen down, and rather quickly. I kept eye contact to a minimum and rode right up to the immigration office. I think was helpful in appearing to know what I was doing. And when i was off track, i knew the touts would point me in the right direction in order to appear knowledgable.
While it is rude, I generally didn't exchange pleasantries and just said "Peru" whenever asked where i was going. When I needed to be, I was very assertive with those who were insistent on helping. On occasion, this meant physically pushing through those trying to stop me.
Remember, these are not volunteers. They are agents who will extract every margin possible. They feed on uncertainty. They can be useful when you wish to do something quickly. Otherwise, government officials will always tell you the next required step.
Always keep a reserve stash of $100 USD in your boot or some other place. Always replenish.
Bring 30 copies of your passport, title, and license.
Finally, remember that most nearly any mistake you make will be caught by an official on the way out, so if you're allowed to go then everything is fine.