Question about 1988 Toyota MR2

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I have a 1992 MR2 G Limited Automatic. I had a reconditioned engine put in it in 2009 due to the original one having a head gasket problem and have had niggly problems ever since. Firstly the car seems to pick the wrong gears when cold and doesn't start away in Drive. You have to manually use 1, 2 and then Drive for at least 10 minutes of driving. Once warm, the car's great. Should I get someone to replace the thermostat - I've read some other leads which suggest this! Secondly, it seems to run/smell hot and ticks when you've reached your destination. Someone said 'they all do that' but I'm not entirely sure - do they normally run hot. Could it be why the head gasket went on the original engine. Thirdly, in Nov/December the alternator packed up - so I had it reconditioned and decided to garage it over the winter and keep it as a summer car. It was MOT'd in July and started being driven again. It's now August and the alterator seems to be on it's way out again - wipers slow, electric windows slow and lights all lit up on the dash. Is everything above all related?? I haven't a clue where to start.

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