Need some pickup recommendations

TB-5 Duncan Custom. Works perfectly in mahogany. They call it a "PAF on Steroids" tone. It'll do rock and metal just fine.
 
+1 for the Custom. I've got one in my Schecter Scorpion (mahogany) and it slays - it replaced an Invader, removing a lot of boomy low end and gross resonant peaks in the highs, leaving me with a tone that can actually make use of a tube screamer without sounding shrill.

Not sure about a cover, but I'm pretty sure you can find aftermarket pickup covers from places like AllParts, or even Amazon or eBay.
 
I know that you are not a fan of the JB... Did you try it in a mahogany body?? For me this is a killer combo for versatility!!
 
I know that you are not a fan of the JB... Did you try it in a mahogany body?? For me this is a killer combo for versatility!!

The JB is hit or miss in mahogany. I just got a couple of Schecter Blackjacks and pulled the JB out of all of them. (Also pulled the 59 out of the neck as they were too boomy.)

:devil:

In *one* of them, it sounded acceptable. The others had that weird upper mid spike that JBs have. In alder that usually balances perfectly.
 
Don't rule out the Seymour Duncan '59 in the bridge position. It's great for rock and can handle metal just fine too (ask Bill Steer). :)
 
The Custom/59 hybrid is a pretty awesome pickup. I find myself wishing it were a little hotter but when Im using a boost in front of my amp its a non issue.