I thought you said you just upgraded the master cylinder? Very hard to say without seeing the car. First you need to work out what is happening. Work out if your brakes are being partially applied then work out what is causing it.
You could have a seized caliper or could be master cylinder related. Jack up the car and spin each front wheel, see if they turn freely. Could be a simple as your handbrake not properly adjusted after your caliper swap and being constantly applied on the rears...

Okay, here's the deal a few days later.
Correct rotors arrived.
Installed them, got the calipers on, re-flushed the fluid and took it for a quick drive round the block. Still rubbing lightly.
get home, jack car up, none of them are spinning freely. They turn with little effort on my part, but aren't free and you can hear the pad rubbing the rotor. At this point (aside from wasting just over half a Litre of high-temp fluid), I decided to just put the Gen 2 brakes back in. (This is proving harder than expected just because the rear calipers decided to push out and now i need to wind them back in too).
right now, the only thing i'm missing is the Gen 3 booster, functionality-wise. Everything else has been correctly lubed and installed.
At this point, i'm about ready to just give up and leave the Gen 2's on and cut my losses before i spend any more time and money...

Hi Joe,
If I were you, & keeping in mind you need the car on the road like yesterday (im assuming), & track day is only 1wk away, I would be doing just as you have suggested.  
 
Put the originals back on, then after track day, slowly start putting back on, eg, start with front rotors / calibers, test see how it goes, then go from there.  Unfortunately it is a process of elimination.  

Yeah, at this point, that's what I decided to do.
Patience is wearing thin when stuff like the old calipers suddenly not fitting happens though
It'll be back on the road before work tomorrow, and if not, I may set it alight and watch it burn in my carport...

If you do burn it... I have 2 for sale.  Pick either one..

I'll keep that in mind
Care for a swap? That green one was good fun to drive, I'll give you that :P
I'll take my running gear out and put it in that thing! It'd be a mad street/track/touge car!

^^yeah wouldn't it.. heres how she looks with ya old wheels on it.
 

They don't look too bad on, actually... Didn't work out particularly nice on mine. Being grey, it looks too monochromatic
 
UPDATE: second test drive, got to some speed (about 80 or so), front rotors were pretty bloody hot after that, rears still have minimal heat, but it's there

If all four brakes are being applied its got to be master cylinder related. Your plunger in the master cylinder might not be moving back far enough. Because your fitting new pads and all I assume with this upgrade, the pads will be really thick and because your old set up probably has worn pads (thinner) it pushes back far enough before getting stuck to not cause them to keep rubbing.

^^ you know, given it's the only thing I haven't changed back, that would have to be it.
I've bought some (more) fluid, just cheap stuff this time. I'll change it back over, and hopefully problem solved!
 
I merely assumed that a BMC being sold in good working order would be in good working order... That said, how do you check without actually installing it and finding out it doesn't work?
 
#brakenoob