From what you say I don't think you'll have any big problems. I'm just completing my latest Cobra wiring now using one of these, but this is the one wired for Ford alternator so is proving a little... interesting.
Making up a loom yourself would be a very expensive way of doing it, I reckon. Also, you wouldn't be able to do the cotton braiding outer cover, you'd have to do it all in wrapped harness tape. Which is fine, but...
Yes, the alterations you suggest are pretty much what I have done. For fans etc. I make up a small ancillary harness to route alongside the main one. Beware of asking for extra wires in the main harness, as this makes it much stiffer and hard to work through gaps etc. (ooer missus). I asked for heavier main charging circuit cables to handle greater alternator output and it's proved a real pain, especially with things like ammeter connections.
It's worth telling Autosparks where you want the DB10, and also what alternator (dynamo, if you're mad) you will use etc. Give them as much info as you can, but be prepared to modify bits - the originals were so variable, they can't be expected to get it just as you want first time. It's not like my Cooper S, where the loom for that model just fits perfectly, down to mass production. I use Autosparks for all my harnesses if possible and have very few problems.
The PRS7 wiper switch is probably the hardest part to find, and I have yet to discover if converting to negative earth is going to affect this - hopefully not, as many XKs have been converted. Be aware there are a number of PRS7s, some are light switches and are different. The correct type has several screw connections on the base.
Fuses - I use the same basic setup as p.52, i.e. one for heavy current permanent lives (browns, etc.), one for switched ignition lives (whites and greens), one for lower current permanent lives (reds etc.) and I use the fourth for the mods, i.e. horn and fan relays.
Here's the MkIII diagram - much more use:
Just noticed, this says 'negative earth' so wipers etc. should be OK. Wiring the wipers and switch is complex. If you search some of the XK Jag sites you should be able to find which goes to where on the switch. Also some 'interpretation' is needed of the colours.
I keep editing this and it's getting longer and longer, so that's it for now!
Roger