I would start over to replace the parts
The weight on the flapper valve needs to be facing UP.
You can download and print the parts list and exploded drawing for the pump from here.
http://www.raritaneng.com/pdf_files/ph_II/L04Ephiiv0303.pdf It shows the correct orientation for all the parts. Remove everything you've removed/replaced and start over, paying careful attention to it.
How old is your toilet? 'Cuz it may just be coincidental that the air valve--part # 1203w...it's a little flat square nut with a hole in it on the front of the dry/flush valve housing--also needs cleaning and/or replacement. A failed air valve would let you bring in flush water, but would create back pressure that wouldn't let you empty the bowl. However, I'm guessing that putting the parts back where they belong and aimed the right direction will solve your problem.
However if your toilet is at least 5 years old and has never been rebuilt, now would be the time to do it...while you have the pump apart.
Stu, I don't think he opened the dry/flush valve housing...take a look at the drawing, you'll see that it ain't nothin' like a Jabsco...it really is a valve, in a separate housing on the front of the pump, and operated by a knob, not a lever.
I'll email a link to this thread to Vic...he'll weigh in with advice Monday morning.