OK, this is how it started. First, I started it up and drove it down the road for about a mile and a half. All of a sudden it loses power and sounds like one of the plug wires popped out. Then I slowed down but before I hit the brake it died and was now coasting. Then it smelt kind of funny like a burning smell but it was only for a second. I got out and of course it was dark in the morning, the wires were fine and I couldn't see anything that was too obvious just by looking. It turned over but sounds like one of the cylanders is missing. I checked the plugs they were fine but I did a tune up just in case. Still nothing and it sounded the same. Now I had a buddy tow my car home and I've done a few things to it. I checked the timing and timing belt, everything lined up and the belt was intact, the belt looked a little loose but I don't think loose enough to jump time and enough to not have my car start. I replaced the distributor including the coil and the ignitor. I took the intake apart and the injectors are shooting gas but, to be honest I don't know how much gas is supposed to be shot out, but it was squirting. I took the valve cover off and all the springs were moving, I'm not sure if that is something that will determine the problem. The battery is fine, and the battery connections look fine. The idiot light doesn't stay on at all, and I have checked every fuse that I could find. That's pretty much all the info I can think of right now. It's a d15 sohc. Please I am so frustrated that I bought a new car that I don't think I need, or want but I need a way to get around.

Running through the tests, in sections A and B below, should lead you to the problem:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-46563.html

Begin by properly testing all under-dash and under-hood fuses with a test light or multimeter. Here's how:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-46563-3.html#post252145

Next, check for codes, perform the K-Test on the ECM, and check for spark.

I do have spark I've taken out every fuse with the little puller and checked for and breaks or blemishes

You need to test for power through the fuse. Visual inspection is inferior and can be very misleading.

Would the fuses and the results of the k test tell me why it sounds as if the engines skipping a cylander?

Not likely. I'm not sure what you mean by "skipping a cylinder." Do you have a vacuum leak?

Where is the vacuum and how do I check for a leak? What I mean is, when it turns over its like it stutters, the only way I can describe it is like morse code. Normally when it turns over its like dot dot dot dot, now its like dot dot dash dot and so on.. hopefully you know what I mean?? Another problem is when I went to check fuses and do the k test my damn battery was dead, I have 3 and all are dead, good luck huh?

It almost sounds like your problem is the battery. I would place one on a charger for a while and see how the ammeter cuts back. If everything looks good, just keep charging it for a while; otherwise, buy a new battery.

Could the battery be dead because the alternator failed?

The first thing you need to do, before working on any car, is make sure the battery is fully charged.

I've recently installed a new alternator, but I was playing music when I was working on it. I left the door open one night and the dome light was on. But I don't think it's that, I mean does the 100 percent charged battery give more spark? And if it does would it not start if you got less spark to the cylander?

And, where is the vacuum and how do I check for a leak?