Ok. So with the rewire

Are there any suggested upgrades I should be making?
Is there a blade fuse box that people have recommendations for?
is there a 65amp alternator or higher that’ll swap in for the 45amp without any modifications?

Have a look on carbuilder solutions site lots of bits...iv'e used the led blade fusebox...
 
There is a Durite fuse box thats a pretty exact replacement, I will try and get a link after tea, Alterations, lots and lots, it depends on how confident you are about your wiring skills, the heater for instance, not only is the wiring just stupid, the plenum could be done away with altogether and everything piped up instead, its would be very easy to do, not cost much and put the heat right where its required rather than into a big heat sucking plenum instead.
Headlamps on relays, heater on relays so the amp sucking wiring wont slow down the motor,
The alternator, if you upgrade it the wiring will only matter until you pull more amps than it can handle, alternators dont just chuck out their rated amps, it doesnt work like that. I very much doubt you will be pulling 65 amps at any one time, I very much doubt you would be pulling 45 amps at any one time, I would concentrate more on making the existing charging system more reliable and efficient, its a fairly easy process and I can talk you through it if you wish. More important than changing the alternator would be to fit a bigger battery, the 072 batterys fitted to Defenders is just simply crap and not up for a large diesel engines starting requirements, they die fast, I will check mine for you and get you the battery number off of it, also, a larger KW starter motor is a good idea, I fitted one to mine and the engine turns over like its got a broken cam belt, I can have a look and get you the part number, or , if you search my user name and add battery (for the battery type) or starter (for the starter part number) you will see my posts with the relevant information.
 

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