I have looked into both and figured in CA, its better to rebuild as any kind of swap is gonna take some work to get it to pass smog/ get it reffed. . .
I hear it is best to keep the same vin, right now running a different Ls motor, but not JDM. . . planning a rebuild on my stock LS just to keep my vin the same. I heard once you slap a JDM in you have to take it to a ref to get it checked to ensure you will have no issues with passing smog. . . but most places don't check the vin on your engine to make sure it matches the car, so it may not matter unless you fail smog and have to figure out why. . .
It should run the same, but you have to change out the engine harness as the JDM harness inside and engine bay is different from USDM. If memory serves you will only have to change the engine bay harness. . .
Anything you change on your engine will make the car run different, some things you can feel the change others you cannot, it is just the JDM engine is made to different specs and not so may regulations, thats why they are faster. . .
I think a rebuilt will run just as good as a swap. . . if you are replacing warn parts, then those replaced parts will be in better condition than the parts in the swap with 30 to 40k on em. . . Also you have a honda, these engines are made to last, my stock went out at 157k(actually took too long to change oil and lost lubrication, so head heated and spark plugs expanded, once I get the holes re-threaded and broken plugs removed it will be ready for my rebuild) if the plugs didn't expand my engine would still be running fine. The engine I put in had 93k on it and it runs the same. . . As long as you take care of it, maintenance wise, it will run great for a long time. . . Think about it that motor with 30 to 40k will eventually have 180k on it and if it is taken care of, it will run just the same. . .
As for the "frankenstein" all that is, is putting a VTEC (GSR or Type-R) head on a non-VTEC block, so you could not use your block, but can use your head. . . For me, I think the head is easier to work on, but have not done any block work yet. . .
If you are gonna spend money to do anything to your engine, and care about the engine lasting, you should just upgrade to aftermarket parts that add more HP, because "frankenstein" you have to do block work to ensure the block can handle the head and to ensure the pistons don't hit and if you are gonna do block work, you would be better off upgrading your internals in your GSR block then downgrading and doing the same thing to another block. . . Same goes for the head, why buy a rebuilt one if you can upgrade the current one. . .
Basically, if you do internal upgrades, you will be replacing everything you would when you rebuild anyways, but now getting more Hp due to the upgrades. . . I was thinking about a JDM swap as well, but then figured I can build my Ls with the $2500 i would spend to get a JDM B18C. . .
So if your gonna spend the money its up to you. . . 1 go JDM and have someone else do the work for you and just drive away or 2 upgrade internals and rebuild (this way you can play some part in the work and get to know your car) and save a little $$$ depending on your upgrades. . .