If you can somehow get the save file over to your PC, you can use PKHeX to edit your save file. (Make a backup!) Making a machoke a machamp should be as easy as selecting your machoke, right click it, View it, change the species from machoke to machamp, and then right click your machoke and set it. Then save and replace the save with the new one.

I would keep Aron for the eventual aggron

Now to deal with your water problems. Wingull is flying/water, lombre is grass/water, mudkip is water/ground.

Mudkip / Swampert is a great pokemon and you should keep it. I'd replace Lombre with Breloom or Roselia, brings your grass/water to grass/fighting. Breloom's mach punch is SWEET.

So to your flyer, the problem with Pelipper is that its Attack stat is pretty awful and ALL flying-type moves in Gen 3 are considered physical. (Water are considered special, which is Pelipper's second-best stat). So keeping Pelipper to primarily use for flying-type moves is going to be rough. Swellow is a great default, and other flyers (Altaria, Tropius) are available later but are either rough to level or not worth it.