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You can do either actually...It depends on the equipment you have...I have done them both ways though and I personally think it is sometimes easier to do from the top..
i've done it both ways...under was better to install and remove (much easier to position as both the engine and car were level) but you need a shop with a car lift...with a cherry picker it was harder to put in (even with a leveler)...but once you get used to doing it becomes 2nd nature
i did not do my swap.but im 95% sure that you can do either.the stock motor is small enough, to lift the car up around it with a lift. but most people dont have access to a car lift at there homes so they borrow an engine crane or buy one for around $170 bucks .....oh sh!t im a little late oh well.
I prefer to do it from the bottom. Drop it out the bottom, and put it up from the bottom of the car, and use an Cherry picker to lift it up through the engine bay. It's a lot easier getting the mounts to line up.