Al Right I have a 99 civic ex with a knocking motor
I would like to swap the tranny and engine
SO What would be the best fit with the least amount of problems.

 

The best fit for any car engine is to replace like with like. Honda's engines are replaceable from certain years to certain years, a salvage or engine shop will be able to tell you, also if you look up honda engines for your year car in Wikipedea it will tell you years and engines used.
If you can get a an engine from a newest year it does have a bit more horsepower but still like engine for fit and harness this is good.
Honda seems lately that each year the new car comes out with a few more horsepower.
So like engine to like engine is the best. Be sure it is an american designated engine. Japan sells a lot of engines to the US, but some of the components are not the same. A salvage yard that took the engine out of a US sold car has the same. If import you may run into few replacement part problems.

 

yeah your best bet for quick and painless is to get another D16Y8 and swap engine for engine. There are many motors that can be swapped with some modification but if all you want to do is drive your car again get the same motor that the car came with.