I had issues to resolve after the first engine start, with the main one being a high idle of up to 2000rpm - even when the engine was at operating temperature.
The main offender was the wax stat - the wax-filled valve (just like in a coolant thermostat) underneath the throttle body which when cold, allows air to bypass the throttle body and idles up. As it heats up (via a coolant feed) it closes the valve and reduces the air bypass to drop the idle RPM. It's a primitive cold start system and notoriously unreliable when they get old.
Normally it would be tricky to delete the wax stat as the standard engine has four auxiliary air/vacuum valves (for A/C, power steering, idle up) all connected to the wax stat/throttle body assembly, but I'm not using A/C or power steering in the Mini so I only have one valve to reconnect. The coolant lines to the wax stat were also no longer needed.
All this meant that I could make a simple blanking plate (and a custom hand-made gasket) however I did have to weld in a single port into the plate - for a vacuum hose that leads to the remaining idle up valve.
I also checked all the vacuum hoses attached to the intake manifold. I used a Mityvac pressure/vacuum pump for pressure testing and found that the MAP sensor hose had a small hole, and so the vacuum hose was replaced.
With everything bolted back on and the engine warmed up, I adjusted the idle to 900 RPM

Another issue was the few oil leaks that developed after running the engine for a while. One oil leak ended up being the result of the valve cover nuts that not torqued down properly and allowing oil to seep out of the valve cover gasket. The other oil leak was seeping down the gearbox sandwich plate, which may indicate a leaking rear main seal. It could also simply be a leak from the sump seal but it means removing the gearbox (and maybe clutch) when the engine is next out of the Mini.
The alternator was the last issue I found whilst the engine was running, as the pulley on the alternator was misaligned with the crank pulley. You could visually see the belt moving side to side as it tried to jump a groove in the 4PK alternator pulley. It's hard to notice the misalignment however when I placed two steel rulers up against the cam gear and alternator pulley, it was then obvious - by approx 1.5 degrees. It'll be much easier to resolve this with the engine removed.
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