Hi Steve,
I’ve been using sildenafil for quite a while now, and honestly I haven’t had any serious side effects — just the occasional mild stuff like a bit of flushing or a slight headache, nothing that sticks around or causes problems. Your symptoms (stuffy nose, dry throat, red eyes) are pretty common and usually just annoying rather than dangerous.
As for progress after surgery, it really does take time — sometimes a year or more — for nerves to wake up again. The fact that you’re getting some morning erections is actually a positive sign. If the side effects bother you, you could try lowering the dose, taking it with plenty of water, or discussing a switch to tadalafil with your doctor — some guys tolerate that one better. And keep using the pump regularly; rehab really does help in the long run.