I would not bother lowering a civic vx, I lowered mine around 1.25" and am thinking about going back to stock hight because the ride is harsh and bumps not being absorbed by the suspension slows you down/lowers mpg, it also makes it so you can get stuck in the winter, as snow can get packed under the car and leave the wheels spinning.
swapping a tranny is easy, took about 6 hours when I did mine and I had never done that before, I did the axle seals at the same time, a new clutch, scoured out the clutch cylinder, resurfaced the fly wheel, power washed the new/used tranny so I didn't have gunk falling in my eyes and installed synthetic MTF fluid, I did this all when my vx had 230,000 miles on it at a cost of around $300 in parts (tranny, axle seals, axle c-clips, clutch, fly wheel work, fluid, taking the tranny to a car wash) it could have been done cheaper but I wanted to make sure everything was going to last another 200,000 miles, a vx/cx tranny is the best way to go and the main shaft bearing seems to be what goes out on them, car-part.com is where I got my used tranny.
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