Luggage and bags:
Since you will be lifting your bags on and off of the train (unless you pay the porter) I recommend taking 2 small to medium soft sided or duffel bag luggage.
Clothing/Shoes/Weather Gear: Layer clothing is most practical. If you are doing an 8-day trip 2 pairs of lightweight fleece pants, 2 lightweight fleece tops and a heavy fleece jacket. The weather is usually cooler in the night and early morning and warmer in mid-day. My only shoes are the waterproof type.
Toiletries and Medical Supplies: If you are from a more humid area (as I am) you need moisturizer daily as the air here is very dry. I always bring insect repellant especially if you are in El Fuerte as the insects are horrible if sightseeing around the El Fuerte River.
Photo Equipment: I have a Sony CyberShot 7.2MP with zoom with extra lithium battery and memory cards. You will take a lot of photos due to the scenery.
Miscellaneous: I always carry Baby Wipes to wash my hands and more hygenic than toilet paper.
Toiletries and Medical Supplies: Since I live in a humid environment (Florida) and not acclimated to the dry air, my skin was constantly dry so a good moisturizer is essential.