This might help. Some great info here, but it is a little dated.

Central America Ride Planning and Road Wisdom - ADVrider

All the advice here is good.
Anyone who has not been there cannot imagine the frustration and anxiety of crossing a Central American border, in the heat and humidity, noise, dirt, and crowds and general chaos.
I did alot of research before our trip and "thought" we were prepared.
I had a list of spanish sentences, like, "Donde es el officina de Aduana?" but as soon as I opened my mouth my poor spanish gave me away.
Unfortunatly you have to resort to "No Gracias" very loudly and firmly to get rid of the "helpers".
Then you are on your own to decide which way to the office you need.
By the time we reached Honduras I had a pretty good routine of how to get through.
There ARE Real Helpful people at every border but it is very difficult to tell who they are. Most will point you in the right direction, and if you get three people saying the same thing odds are you are on the right track.
Immigration is usually free, and my tactic was to watch the other people ahead of me in line to see what if anything they were paying.Usually if there is a cost it is posted, and very cheap, $1-10.
Always loudly question "why"(por que?), when asked for money.
Aduana(customs) is a little different, as there are more oportunities to get money from you.
Sometimes they pretend not to like your paperwork or want to strip search your bike.
I was always Pleasant and persistant( I usually freaked out before and after crossings) that every thing was OK and that no money was forthcoming.
This worked every time except the Military checkpoint just south of the Costa Rica-Panama border. The "Jefe" was determined to get something from me. So alone in his office with five of his men he asked if I could help them out. It was very hot and I asked how much cost in Panama. He looked surprised and said .50 cents so I handed him Three of the five dollars I had and told him to buy everyone a . He laughed and took the money knowing we had reached a stalemate. All of his men knew how much he had taken from me and what their share was for. Plus it had cost me alot less than what he was hoping for.
You will find that Latin Americans have a great sense of humour and "if" you can keep yours it goes a long way to smoothing out procedures.
Bien Viaje

Wow, great advice, could not have summed it up better then that.

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http://www.journeyrider.net Latin America blog (07-8)

I know posting a reply this late will probably not get to everyone who helped or respnded, but I do appeciate all the advice.
I am starting my way back towards the states tomorrow and of course the first thing is to try to handle this crossings myself with no handlers, the other will be be as prepared as I can be understanding they could take some time. Also looking at other border crossings (less frequented) maybe a way to go. It is too bad for all the beauty and adventure down here that it all comes with the same amount danger and hassle.....
Anyway I will be posting as I go, at freedomthrumovement.blogspot.com and also one question if anyone reads this is if you do do the borders yourself without handlers does this mean you have to get in that long line behind all the trucks and wait, or can you just drive to the head of the line, park, and then start the process with migration and then customs, in that order....... thanks again

Always ride past all the trucks, cars, etc and park in front of the immigration/aduana offices.

In fact, when you are on a motorcycle, always ride past *any* line of vehicles. Use the opposing lane, the space between cars, the shoulder, whatever. Of course, be careful. The rule in Mexico, Central America, and California: Motorcycles go first (if they can get there).

Jeff

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SF to Panama and back
How I Nearly Killed My Friends In Baja