1998 honda prelude with euro r swap

So I just recently bought the vechicle, and owner had down the euro swap on it. the car runs fine, idle stays around 1000 rpm's, vtec hits around 5500rpm's, throtle repsonse is great, etc..

I went to emmsions and my computer wasnt linking up to the cade scanner/diag computer.

So i hooked up the old one and it links up, awesome, so im driving home and the check engine starts flashing, (damn), so i took it to auto zone and got P1399 and P300.

To summarize, the codes were blocked egr passage, valve clearance out of range, fuel system concern, ignition system concern, MAF sensor faulty, HO22/AF, and clocked intake or exhaust system.

Could the codes be popping up because its a different engine? could I actually have those problems even tho my engine seems to be running just fine? is the computer screwed?

is there any differences in timing between euro r h22 and the original h22.

I need to get past emissions, any info you have would help. thanks.