OK, lets start by correcting some terms. The structural members you want to raise are not rafters, they are ceiling joists. You are right that because you have balloon framed walls, that has no effect on the top layer of ceiling joists. Changing these joists have no effect on the balloon framed walls.
The thing you have to determine is if the ceiling joists are tied to a load bearing partition somewhere near the center of the house. If you have full roof rafters with a ridge board, it is very unlikely that the ceiling joists are tied into any down supporting bearing wall. Raising them should not be a problem if you plan for support of these joists if there is any center resting point, via a knee wall on the center resting support. If these joists span the entire width of the structure, then you can safely shorten them and reconnect them to the roof rafters. They serve two purposes. First a ceiling joist, and second, a collar tie for the roof rafter. I think you will be fine, however, I'd love to see some pics of the attic area with the joists. Good luck.
Since you're putting a gable roof on it, I can only assume this is being built for storage purposes, not for aesthetics.
Building it with a glulam ridge beam would be more difficult, but it would be much stronger. The main issue with a ridge beam design would be lifting the beam into position. If you can manage that pretty easily, the rest would be a breeze. I'd put some ceiling joists up at either end, lift one end of the beam over one of the joists, pushing it far enough to clear the ceiling joist on the other side, like so...
B
B
B
JttJttJBttttttttttttttJttJttJ
S B S
S B S
S B S
bbbbbbbbbbbbbbbbbbbBbbbbbbbbb
B = ridge beam
J = joists at the ends of the barn
S = studs at the ends of the barn
t & b = top and bottom plate
... and then lift the bottom end of the beam up with some ropes. The joists will need some strength to support the ridge beam, and you'll need to be able to stand on them, so I'd use three 2x6's @ 9" OC on either end (where the outermost "2x6" is actually the top-plate of the walls on either end of the diagram) with some 5/8ths plywood on top of them. I'd toss in some temporary studs at the center point to make sure the joists hold up to the weight of two people and the ridge beam. Once the beam is in place, put in the ceiling joists and plywood on top of them to make walking around easier (and to create an attic for extra storage,) then put the rafters up.
Grab some metal brackets for the joists, rafter heels, and rafter/ridge connections (it'll cost you an extra $125, but it will make the structure a lot stronger) from a HI store and your little barn thing will be able to withstand some nasty winds.
Best Answer
Collar ties go on the top third of the rafters, and mainly hold the rafters to the ridge beam, they may or may not be required by local code, or may not be required if you use an approved metal connector like a Simpson rafter tie.
Rafter ties go across the bottom third of the rafters, in older construction they could be on the bottom half or bottom two thirds of the rafters. They prevent the roof from flattening, and they're pretty much usually required unless the structure is engineered so the outward thrust is taken into account some other way. For example some cathedral ceilings are made to be stable without rafter ties. In most cases ceiling joists are parallel to the rafters and are installed in such a manner that they function as rafter ties.