After much time messing around with this I figured out the issue. It is the way WinDoze (Outlook) formats the HTML E-Mail signature!
I tried publishing an HTML through many ways and it always lost the pictures and sometimes even the formatting. I knew I needed to get it into an Apple compatible format but could not figure out how, copying it just copies the text and leaves out the pictures so here is what I did!
1. Copy the entire signature from an existing E-Mail. (or create your own)
2. Paste it into TextEdit.
3. Save it as a RichText document.
4. Open the document and select the entire signature.
5. Open Mail and paste the signature into a new E-Mail.
6. Send it to yourself.
7. Open that Email on your iPhone. (or iPad) {I have not tried it on an iPad but I assume it will work the same}
8. Click on your signature and "Select All".
9. Go into Settings>Mail, Contacts, Calenders>Signature.
10. Click on the account you want to use or use all accounts.
11. Paste the text into the box.
12. Shake your iPhone and click on "Undo Change Attributes". <--VERY important! (It updates the formatting when pasting)
13. Send an E-Mail and check out your awesome new signature!