1) Anyone w/ ALS that needs respiratory support should be on BiPAP, not CPAP, to have choices as to level of expiratory relief (aka pressure support, the difference between the pressure when you breathe in vs. out) -- max difference on a CPAP is 3 cm and may be less -- if you are on CPAP w/ inadequate PS, you are working your breathing muscles harder than needed. That said, the idea that the more PS, the better works for some pts but not for others, where too deep a breath can be too much work as well. So you need to refine settings as breathing difficulty progresses.
2) yes, dysphagia can be separate from lung function and if you can't swallow well, liquids are more likely to get into the lungs or feel like they are
3) Trilogy is basically big BiPAP w/ AVAPS function & battery. If you don't need a portable machine at first, is overkill size (12 lb, I believe) for home and alarms may be annoying. Even when you need a portable, it may or may not be the best choice depending on what features you need. For people who plan to move to invasive ventilation when needed (trach), getting a Trilogy early may be desirable since it can be used invasively, depending on the speed of progression.
For coughing and choking, also may want to look into suction machine, Cough Assist, Hill-Rom Vest, Acapella device (the blue one). Also, know I sound like a broken record, but always check the humidification level to see if tweaking can help.