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Brandon, I don’t know you and I don’t see a profile on you as a member, so I don’t know if you’re a tech or working on your own equipment. SO…I gotta say this:
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Converting from one gas to another is part of the equipment’s installation procedures, so the manual explains that “Installation and start-up should be performed by a qualified installer who thoroughly read, understands and follows these instructions” in the manual.
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With that obligatory statement said, I’ll go on…
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Along with ryanreid1‘s explanation, be sure you check your incoming gas pressure. Ensure the pressure doesn’t exceed 1/2 psi. That convertible regulator isn’t designed for anything more. If that’s good, then check and adjust your convertible regulator per the specified operating pressure in inches of water column as indicated on the data plate.
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You didn’t specify what you’re converting to, but APW units come set up for NG and require converting to LP. The primary air shutters should be re-adjusted accordingly. You also didn’t specify a model number, which would’ve been be helpful. APW gas units have pretty straight-forward procedures spelled out in their INSTALLATION & OPERATING INSTRUCTIONS manuals which explain the exact procedure you asked about.