So I bought a beautiful 98 2door Accord V6 VTEC Honda and the motor has a knock only paid 200 went on to eBay bought a new motor with less than 50K but from what I understand it's out of a 2000 and I was told I have to do the wire harness in the ECU any tips or easy shortcuts to make this as smooth as possible

 

I don't know all the differences between the 98 and 00 V6. You may be able to swap parts of your 98 onto the 00 motor and use the original wire harness.

 

From what I understand, the differences in the engine are sensor locations. It's the V6 trans that's the real difference, as they are 98 & 99, and 2000 thru 2002. It's mostly in the electronics though. It might be worth getting a Factory Service Manual (FSM from Helm Inc), You'll need the V6 supplement, which has as many pages as the 4 cylinder cars. You won't need the 4 cylinder version, just the supplement. I'd give you a pdf link to it, but like most of the other links posted in the forums, it's gone dead (like those on Honda Tech).
I hope this helps.