Re: Loading a javascript site-wide
For the <a>, I believe you have to put in in your code, just some where in your template code.
Or you can write a piece of code that append that to an element on your page '<a href="http://www.instantssl.com" id="comodoTL">SSL</a>'
I would go for the 1st choice since it's easier 
For the second part, I never tried the body_onload but I dont think you need to put the script tag there if the file is .js. You only have to put the script tag if the file is .php (you can put .php files in the jscript folder)
I no longer provide installation support on forum for all my modules. However, if there are real bugs with the modules please feel free to contact me