BONUS: Also works with salt input/output! If that was included with the others for the metric, the score would be 1447.1 :P

Methodology
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Step Zero - Template Redraw Prevention
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The salt input is directly behind the template input, and both are pulled at the same time by a 6-arm, drawn in the direction of salt->template. This means that after the first draw, as long as nothing but the 6-arm draws from the inputs the template will always be blocked.

Step one - differentiate between element and metal
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The salt/template 6-arm pulls the input element (and blocks the input glyph), which is then placed on a duplicator. A salt is drawn and passes over the duplicator, while the input element is then taken over a calcifier and placed on the animismus glyph. The duplicated (maybe) atom is then placed on the duplicator, and another salt is drawn, possibly modified into a copy of the input element again. This second salt is then passed over the calcifier and placed on the animismus glyph.

If the input was an element (or salt), there are now two salts on the animismus glyph and a mors/vitae pair is created. Otherwise, the template atom stays on the upper part of the animismus glyph.

Path one - Element
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If a mors was generated in step 1, it is used to repeatedly wand an atom off the initial 6-arm. Since a copy of the input atom is sitting on the duplicator, the appropriate atom is wanded off and sent to the output assembly.

If no mors was generated in step 1, the 6-arm eventually fills up, and both the salt and template inputs are permanently blocked.

Path two - Metal
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This is much slower. The template metal is put on a projector, and 5 quicksilver are placed with it. Any quicksilver not consumed are put on a stick. Each metal should eat (5 - X) quicksilver, where X is the number of quicksilver needed to upgrade lead to the template, so the stick can then be loaded onto a wanding wheel to draw the correct number of quicksilver for the copying process. The now gold template metal is transferred over to the lead input and used to wand off a new lead as necessary.

NOTE: The wanding wheel has to be loaded in REVERSE order of the stick creation, which is why a stick is built then fed back in. The need for a reverse load is that a gap in the wanding wheel (including a leading gap) results in bad bonds and a mess - we can only guarantee a gapless wheel if we load it backwards, as if there are any quicksilver to load only the last is guaranteed. An empty wheel is fine.

For each output a lead is placed on a projector and five upgrades are attempted. An upgrade only works if there's a corresponding quicksilver on the wanding wheel. Any that aren't used are disposed of. Once 5 attempts are made, the new output is placed on the output glyph.

If the template was consumed to make mors, the lead input is eventually permanently blocked by its 6-wheel. As for the quicksilver, no input registers the same as gold so 5 are consumed per loop. However, there's no lead to upgrade so all 5 are thrown into the disposal

Output
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The metal processor outputs directly to the output glyph. The element processor is a little more roundabout with a couple of arms passing it around first.

The metal side makes 1 output per loop, the element side makes 3 output per loop.