Lots to comment on here.
I've shipped and received fish several times and never had an issue. It can be tough to keep the heat pack dry, it needs to be open to O2 to work properly, but when wet can stop working. Would be nice if you could just toss it in a Ziploc. I tend to wrap it lightly in newspaper and tape to the top of the box.
As for the cycling bit, I don't know what you mean about the blue pads on the AC110 or is that on the Penguin? I think the AC110 is what used to be the AC500, right? I've not changed filter pads in my AC500's in 5 years or so, and the sponges are going strong. I just rinse every other week. Replacing media is just reccomended by the manufacturer so they make more money. Straight up. I was a terrible salesman at the LFS I used to work at as I told the truth. Just rinse (in tank water) and re-use.
You can just swap pads. There will be enough beneficial bacteria coating the rest of the surface area in the 55 to quickly colonize different media. You'd want to swap it (or rinse the gunk) right before adding fish though, as the bacteria will quickly die off in the 35 without a source of ammonia (fish waste).
As to the order, I emailed N-E Cichlids and got this as the current stock of cichlids. Most fish on the site are from their suppliers and not on hand.
CARPINTUS GREEN 4" $12.99
CONVICT WHITE REG. $3.99
DOVI 4-5" LGE $29.99
G. JURAPARI- LGE $29.99
GALAXY BLUE DEMPSEY 1.5" $34.99
JACK DEMPSEY XLGE $11.99
BLACK BAR RED MIDAS 5-6" $24.99
MIDAS CICH. 5" $24.99
SEVERUM GREEN REG $3.99
VIEJA BIFASCIATUS 6-7" $24.99
VIEJA HARTWEGI 7" $24.99
As for the peas bit, they'll help with digestion but it's not a digestive issue. Some fish may appear to have a swim bladder issue as they'll swim funny, but in reality it's an intestinal tract problem. That's where the peas help. If the fish is eating and defecating normally the peas won't fix it's swimming issue (but won't hurt either).
For the 35 gallon stocking, I'd reccomend a smaller pair of CA cichlids. Myrnae, Honduran red points, or panamensis come to mind. Active, great color, interesting breeding behavior. Though I am a bit of a cichlid nut. And I think A Place For Pets has all three of those in right now, for about $6.99 each.