Why the flatbed it worry? Was there a noise or symptom that led you to believe that the car won't run for the few miles to a shop just as it has for its 60k+ miles? If there was, then by all means flatbed and don't turn it over. Critical to the success of any IMS replacement is making absolutely certain that there is no debris already floating around in the engine.
$4k is twice what I see people posting as labor costs. More common is ~$1k for a manual. More for a TIP as the whole engine/trans unit has to be removed and then replaced. Which might get you to $2k but certainly not $4k. What is his hourly labor rate?
And are you doing anything else while you are there? AOS, water pump, clutch, plugs/tubes/coil-packs, etc?
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