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1) Does the filename include the %20s instead of spaces? It's probably easiest just to convert spaces in the filename to underscores (in both the name in the archive and the name in the manifest).
2) epubcheck doesn't support any form of encryption. When you embedded Times New Roman InDesign automatically obfuscated it and generated an encryption file. This font will only work on ADE readers, and iBooks doesn't support any form of font embedding (I see you mention sending it to Apple devices in your other post). You also probably don't have a licence to distribute Times New Roman anyway, so it's probably best not to embed it - re-export the epub from InDesign and leave the font-embedding checkbox blank.
If you need to embed a font in an epub it's simplest to use one of the free fonts from SIL, Gnu, or other foundries, which can be embedded without the need for any obfuscation.
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