I believe there's a PCM update from Ford for the starting issue - some ST's suffered with it, others not to much.
The transponder receiver is a shroud around the ignition barrel IIRC, just reads the chip in your key when it's in proximity. I believe they just unclip.
Does it do it with both the remote key and the standard blue chip key? You can eliminate whether it's a chip problem or a transponder receiver problem.
Whining rattle noise, could be anything depending on where the noise is coming from. What's the mileage on the car, and what year is it?
Rattling could well be the timing chain needing inspection/replacement, but could also be the bearings on any one of the pulleys on the side of the engine (alternator, water pump, power steering pump, crank), or the release bearing on the clutch (unlikely while moving though).
The previous owner lost the blue chip key I could do with a replacement really it's not done it today but on further tinkering, it seems to do it when the key is a certain way if the buttons are facing me then it works if they face away then it'll be intermittent maybe chips a bit duff?
The year is 54 plate so it's an early model the mileage has just tipped over 80k the clutch is fine I think it was replaced. it is a bit tappety on tick over eliminated that issue though. the only other way to describe it is, it sounds like a small turbo spooling up and it's got a boost leak if you catch my drift?