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I've got an auto transmission. How well will the transmission hold up?
I've had no experience with automatic transmissions. What little experience I have had with them isn't pretty. The torque converter, for starters, isn't properly matched with the newly generated torque. Some users report that the transmission will not correctly shift. As the cost of a Level Ten torque converter is close to that of a 5-speed swap, I would recommend changing to the manual transmission and kiss all of the automatic transmission woes good-bye. There seems to be a huge group of automatic transmission owners who don't want to let go of their non-performance geared transmissions; like I've said before, it's not my money.
That sums it up. Honda auto transmissions are good for an engine in stock form (or with mild mods) but if you plan on going for FI you can forget it.