I did the trip within the last days in both directions - it's OK if you're ordinary size - I'm 6'5" and then it's a little bit more painful.
In addition when I was on the night bus last night (Fuente del Norte) I was really scared as the bus driver was very close to sleep: The last hour (before reaching Melchor de Mencos - Border to Belize) was really dangerous and I was very close to stop the driver. I would never again travel 2nd class: You must travel 1st class and then it still could be rough.

From Guatemala City there are extremely comfortable buses with seats like beds to Flores (ADN - which is a Fuente del Norte company - 9pm and 10pm - terminal just around the corner from Fuente del Norte in the Zona 1). The best way find out schedules is on http://thebusschedule.com/. There are schedules for all countries in the Americas.

Besides the boat option from Honduras there are companies running buses with great comfort - most comfortable is "King Quality" (http://www.king-qualityca.com) and very good comfort is "Ticabus" (www.ticabus.com). Both need an overnight in San Salvador. Buses from San Salvador leave around 6am and arrive Guatemala City around 11am.

Crossing the borders is much easier than crossing the Belize border: In most of the borders you can even stay seated (except the Guatemalan side of the SAL - GUA border).

Best complete overview and very accurate with price information can be found in Lonely Planet. Go to the country of your choice, click on getting there and getting around and you'll find all information (for example for San Salvador at http://www.lonelyplanet.com/el-salvador/transport/getting-there-away).
By the way: Ticabus is connected to cheap and clean hotels in destination cities and the Tica Terminal is even in the building of the hotels. So you get up and just go downstairs to check in in to your bus.

Again another beautiful day in paradise - just smile and be happy :-)