Check your main relay, I don't think you need a whole new harness. You should wait for a few more people to input on the problem.
As for the build, ls/vtec engines are not bolt-on builds. The problem with them is that most people think they are, and their unreliable reputation stems from that. People slap a B18C or B16 head on their LS B18B block and call it a day. The B18B bottom is made for a max rpm of 7200 (I believe is fuel cutoff point) but the B18C can do 1000 more rpm, people then drive them above 7200 rpm and something in the bottom end breaks pretty quick. To have a reliable ls/vtec, you need to build up the bottom to handle the extra revs and power output. They are usually pretty expensive engines to build correctly. If you just want some more fun in your car then a swap would be less labor intensive, and in most cases cheaper. An ls/vtec engine can be made to be very reliable but it is not a cheap or easy process.