The Plan

While this may exceed the patience of most, I am told the process will takes years and a plan should be set. Here are the guidelines I have learned. I confess that as a novice when writing this I cannot claim to back this first-hand. This is one reason my first year of bonsai collecting is having many smaller seedling or pre-bonsai to grow over many years—and expect that some will be weeded out and some may not survive.

From seed, seedling, cutting or air-layering—establish radial surface roots and groom them to grow stronger over time. [Alternate: if air-layer a branch with other qualities, develop good roots secondarily]
If from seed or seedling, cut off taproot to encourage new radial surface root system.
Repotting over time to focus energy through nebari roots.
When repotting, consider using a tile or felt sheet with a narrow hole in the center. Magnesium in fertilizer should encourage root growth. Magnesium is a mineral found in lava rocks, added to soil.
The primary branch should reside close to 1/3 the desired final height (e.g. 4 inches from nebari for a 12 inch tree). If a branch exists there, redirect the branch more vertical to become the new apex.
Ideally not directing towards the front this soon. If the branch directs towards the original front, see if a new front or rotation will still benefit by the nebari.
If no branch exists at that desired point, consider “trunk chop” at that height. The result will hopefully be an array of branches to select a new apex and others as a primary branch.
Avoid a branch projecting from the inside of a curve or directed towards the front, the later may block the trunk from the front.
Grow the base of the trunk in a larger training pot, training box or in the ground. Prevent a deep tap-root if in the ground with a weed fabric a few inches below.
As a pre-bonsai, when the trunk is flexible, wire a fluid trunk shape—or cause the base to move back then return the apex towards the center or in the style of tree you desire. (1-4 months)
The “golden rule” or ideal proportion would be 1/3 the distance from the primary branch to the desired height. (If 12 inches as the total height, and the primary branch was at 4 inches—the secondary branch would be near 8/3 inches, or 2.7 inches higher.)
The result will be a gradual tapering in diameter of the trunk. This may take one season for each increasing node or branch, each narrowing of the trunk.
To maximize girth of the base, you may leave an extra “sacrificial” branch at points along the trunk or near the apex—later to be removed. Select a sacrificial branch that projects from the rear, where the scar would be less noticeable.
A triangular foliage and branch network is desired
Do not allow the lower branches to grow too long without tertiary branches.
Prune and train shorter internodes, and branching close to the trunk—if desired. Encourage light to reach the trunk. Prevent branches to grow longer sections (internode) and foliage away from the trunk. Outer or more dense foliage can cause inner foliage to be shaded out.
Generally prune back to the second node to encourage bad budding and ramification.
General pruning: (1) remove vertical upwards or downward branches, (2) remove crossing branches or directing towards the trunk, (3) tapering branch diameter is desired so if not reducing in width then remove it, (4) reduce the number of branches at a node if greater than two
Prevent “inverse taper” of the trunk, resulting from too many branches growing from the same point. Reduce the network, but be mindful of scars seen from the front.
A triangular foliage and branch network is desired
Do not allow the lower branches to grow too long without tertiary branches.
Prune and train shorter internodes, and branching close to the trunk—if desired. Encourage light to reach the trunk. Prevent branches to grow longer sections (internode) and foliage away from the trunk. Outer or more dense foliage can cause inner foliage to be shaded out.
Generally prune back to the second node to encourage bad budding and ramification.
General pruning: (1) remove vertical upwards or downward branches, (2) remove crossing branches or directing towards the trunk, (3) tapering branch diameter is desired so if not reducing in width then remove it, (4) reduce the number of branches at a node if greater than two
Prevent “inverse taper” of the trunk, resulting from too many branches growing from the same point. Reduce the network, but be mindful of scars seen from the front.

[1] Nebari

From seed, seedling, cutting or air-layering—establish radial surface roots and groom them to grow stronger over time. [Alternate: if air-layer a branch with other qualities, develop good roots secondarily]
If from seed or seedling, cut off taproot to encourage new radial surface root system.
Repotting over time to focus energy through nebari roots.
When repotting, consider using a tile or felt sheet with a narrow hole in the center. Magnesium in fertilizer should encourage root growth. Magnesium is a mineral found in lava rocks, added to soil.

[2] Target a desired height for the tree

The primary branch should reside close to 1/3 the desired final height (e.g. 4 inches from nebari for a 12 inch tree). If a branch exists there, redirect the branch more vertical to become the new apex.
Ideally not directing towards the front this soon. If the branch directs towards the original front, see if a new front or rotation will still benefit by the nebari.
If no branch exists at that desired point, consider “trunk chop” at that height. The result will hopefully be an array of branches to select a new apex and others as a primary branch.
Avoid a branch projecting from the inside of a curve or directed towards the front, the later may block the trunk from the front.
Grow the base of the trunk in a larger training pot, training box or in the ground. Prevent a deep tap-root if in the ground with a weed fabric a few inches below.

[3] Wire character into trunk

As a pre-bonsai, when the trunk is flexible, wire a fluid trunk shape—or cause the base to move back then return the apex towards the center or in the style of tree you desire. (1-4 months)

[4] Select a secondary branch(es)

The “golden rule” or ideal proportion would be 1/3 the distance from the primary branch to the desired height. (If 12 inches as the total height, and the primary branch was at 4 inches—the secondary branch would be near 8/3 inches, or 2.7 inches higher.)

[5] Again, select a new apex at this node

The result will be a gradual tapering in diameter of the trunk. This may take one season for each increasing node or branch, each narrowing of the trunk.
To maximize girth of the base, you may leave an extra “sacrificial” branch at points along the trunk or near the apex—later to be removed. Select a sacrificial branch that projects from the rear, where the scar would be less noticeable.

[6] Once the base and trunk is established, develop the branches

A triangular foliage and branch network is desired
Do not allow the lower branches to grow too long without tertiary branches.
Prune and train shorter internodes, and branching close to the trunk—if desired. Encourage light to reach the trunk. Prevent branches to grow longer sections (internode) and foliage away from the trunk. Outer or more dense foliage can cause inner foliage to be shaded out.
Generally prune back to the second node to encourage bad budding and ramification.
General pruning: (1) remove vertical upwards or downward branches, (2) remove crossing branches or directing towards the trunk, (3) tapering branch diameter is desired so if not reducing in width then remove it, (4) reduce the number of branches at a node if greater than two
Prevent “inverse taper” of the trunk, resulting from too many branches growing from the same point. Reduce the network, but be mindful of scars seen from the front.

[7] Reduce leaf size, needle size or internode

The more ramification and leaves will reduce leaf size—distributing energy.
Depending on the species, timely de-candling or pruning new growth will force branches to emerge closer to the trunk or train shorter leaf or needle size/length.

[8] Contained in a shallow pot, replacing inorganic soil will slow down tree growth

Shorter trunk & branches
Shorter internodes and more dense ramification and foliage
Requires fertilizing and frequent watering

[9] Avoid killing the tree

If the tree lacks character or key features, move on to other trees.
Avoid sunk cost that it takes too much effort to correct or recover—mark it up to a lesson and move on.

A formula for desired branch placement is an adaptation of proportions selected by the 'Golden Section':

First branch is at approximately 1/3 the desired finished height
is at approximately 1/3 the distance from the first branch to the finished height
Third branch is at approximately 1/3 the distance from the second branch to the finished height