Ok, to try and simplify things for you (hope I dont confuse you more, its really not as confusing as it sounds), theres a few things you should know about US engines vs their JDM counterparts...

JDM, stands for Japanese Domestic Market, this means the engine has been imported from Japan, and is not available here... The downside is that since its not from a car found here, you cant simply go upto Auto-Zone and say "yea I need a whatever part for a 88 CRX DX", you have to find out which part to ask for... This isnt really that big of a deal, and MOST parts are interchangeable between D series engines, be they JDM or USDM...

USDM, stands for United States Domestic Market, this means the engine comes from a car that is found here in the states... So its much easier to get parts... You simply find out which car the engine came from (lets say a 92-95 Civic Si, which has a engine code of D16Z6) and goto Auto-Zone and ask for say a timing belt for a 92 Civic Si...

Since you probably wont be working on your car anyways, it really dosnt matter... This is mainly for a do-it-yourselfer that has to be conserned with this... But its good to know, incase your technician might not...


As for engines (for his quoted price) heres a list of good engines in that price range:

JDM engines:
DOHC ZC
D15B with VTEC (there is a VTEC-E model, make sure its not VTEC-E, and is VTEC the power implimentation)
SOHC ZC with VTEC


USDM:
D16Z6 (comes from a US spec 92-95 Civic Si or EX)
D16Y8 (comes from a US spec 96-00 Civic EX)

As for a warranty, usually they warranty the internals only, such as piston rings, bearings, ect... Stuff inside the engine... They usually dont warranty the sensors, or external parts, distributor, starter, ect...