with the coil wires you can either use the mk2 wires, or the mk3 wires. its totally your call

you'll find that the mk3 plugs and the mk2 plugs both have the same pins in use, so if you fit the mk2 coil wire you'll need to splice the mk3 wire to it. this is because the wire on the mk3 plug also does a few different bits on the mk3 loom, isv, ecu, etc. mk2 just does the coil. I use the MK2 wire because its chunkier, though the mk3 wire will probably be ok.
if you use the MK2 coil wire, follow the mk3 black wire back till you find where it comes from, and chop it out. on the mk3 you'll see there is a joiny piece where several black wires all come together, you'll know what i mean when you see it. if you use the mk3 wire, simply crimp a spade on there and pop it onto the mk2 coil

on the mk2 coil plug, you'll see there is a short length of red/black wire with a spade on poking out the back, this you can chop off as its only needed for the 16v isv controller. you could just leave it on but unplugged if you like! the main red/black wire which runs to the fusebox is the rev counter wire yeah, you need to keep this. the mk3 loom will have a wire to this pin too, this is from the mk3 ecu and is not compatible with the mk2 clocks, so chop it out.
aye you chop out the purple wire, and just leave the vac hose connected up to the clocks as per std mk2 16v.
The blue wire is the alternator charge wire, but its to
F/3 
the reason you're confuse is because on the mk2 the alternator wire is in the lighting loom, you'll see it neat to the battery +ve. on the mk3 this is moved to the engine loom, so in effect you now have 2 alternator wires! you can use either one. i use the mk3 one cos its neater, plus it uses much better waterproof connectors so no more corrosion damage. the other plug is the reverse light switch

F/1 is a red wire, this is a starter motor live which is required for the MK3 ECU, so I think you might have got that one confused as well? F/4 is an earth, on the MK3 its for the speedo sensor. Reverse lights are to F/6 and F/7
the big connector block under the header tank is the radiator fan control unit, i bin this altogether and keep the mk2 fan wiring. the single pin sensor you mention is the after-run switch aye, i leave it disconnected.
this last plug is for a breather heater, which isnt fitted in the uk. follow the wires back from it and chop it out
