ojmagg,

A quick search on google would be your best friend. I was able to find enough info to get you started as many have done this. The major difference would be space and ours being vertical.

1. I am wondering about attaching the mold to the MDF...how should I do it? Should I glass the whole thing...or would a few tubes of construction adhesive work?
IMO, I would suggest to glass them together. The question is, how thick is the mdf you are using going to be. Also, if you are already glassing, why not scrap the MDF and just glass what was supposed to be the mdf section. I'm not sure about clearance with the stock cover when using mdf. IDEA, tape up the stock cover, wax it, glass it, pop it out and glass both molds together?! That will look pretty clean if done right.

2. How do I line up the mold and the MDF cover? I'm thinking about placing the mold in the tire, then throwing some construction adhesive on the mold, throw in the MDF, then put the stock spare tire cover back on...
That would be the easiest way to combine the two together, but I would still glass it after.

3. How do I get the holes in the MDF and plastic cover to line up perfectly?
My answer to question one could eliminate this. But if not, it shouldn't be hard to find the center on the back of the cover (with tire mold), I'd cut the plastic cover first and trace that onto the mdf then cut.

4. How should I cut the spare tire cover
A router and circle jig with the right bit should work, I would definitely cut it a tad smaller and then sand out the rest.

5. What is the best sub to use? Pushing about 150 watts RMS...crappy old Dual XPA2100
This would be a personal preference. You would probably want to look for the slim line subs available today, you might have enough room to countersink the sub. If you look at my blog, you will find the router and circle jig i made as well as the countersink i'm talking about. The subwoofer I am using is the Pioneer Slim Line 12".

6. What about a grill guard...how should I attach it...I punctured the last speaker.
Grill Guard... Maybe someone else can chime in on this. How much protection do you need?