I recommend following the V&H directions exactly leaving the head pipes loose until you have the brackets installed on both sides and the left pipe bracket at the starter. Also use new exhaust gaskets even though V&H says you can reuse the stock one if there are ok. Tighten the manifold nuts last like it says but evenly and carefully. I was able to use a 1/4 drive rachet and 1/2 inch shallow swivel socket on the rear nuts.
As others have stated these nuts will require checking and retightening often. I found if you don't get the slip on's set far enough on the rear pipe at the center of the rear brackets they may vibrate more than stock.
I also ruined a o2 sensor removing the rear one which was factory cross threaded and unbelieveably tight. That cost me $50 before I even got started with the new setup.

Good luck.

 

Got same pipes and been there......Keep it simple by first using the proper gaskets at the heads so the pipes seat deeper in the ports....use ONLY screaming eagle flat woven gaskets.....they are cheaper than stock and much easier to install.

Also use nylock lock nuts available from hardware store....no, the heat will NOT melt the nylon locking inserts.

Using proper gaskets and nylock nuts you will have no trouble with install and they will never work loose....And you will never have to tighten them more than a few ft/lbs just once.

Yeah, also use 1/4 drive floppy and 1/2" socket along with required extension......

 

Dont worry about torque specs on exhaust, tight is tight.

 

Since no one else answered your last question about the pipe being close to the fuse box cover. Thats the only problem with the true duals. Its not bad getting the cover off. Putting it back on is a lot harder. Don't feel you are the only one who has that issue.