On top towards the wire harness of dist. Never noticed this before, installed new seal as well. Should I be worried? Is there a certain order to tighten the three screws that hold dist cap?

 

Are you sure the cap it seated correct on the distributor. If there is a gap water can get in.

 

All three screws lined up. How could I make sure otherwise if it's seated correctly?

 

I'm not real familiar with the Honda distributor caps but most have a notch or pin that positions the cap correct. If that isn't lined up then you would have a gap. But again I haven't looked at my cap on my 90 Civic & it has been years since I changed a cap on a Honda. Like My 79 Civic back in the early 80s. So there is a chance that the cap screws would be in the right position to attach it wrong.
Take off the cap. look at the distributor & see if there is a notch on the edge of it. Then look & see if the cap has a piece that fits in that notch or hole or whatever, they need to be lined up then screw the cap on & set the wires in the right position.
I hope this helps. Update me if what I'm saying is right or wrong.

 

I'm pretty sure there aren't any notches or anything to line up. I've replaced this on my car before which is why I'm baffled. It's making me freak out a bit thinking water could get in

 

i've rechecked everything, seal isn't being crushed, tightened the screws evenly as well. still the gap still exists towards the harness as opposed to the top screw. maybe it's always been that way and never noticed? i don't know but here's a pic

 

That doesn't look bad. Is the cap a Honda cap or an aftermarket cap? It could be a bad cap. If it is aftermarket where did you buy it?
It looks from the picture like the cap is distorted in the gap area. Look at it & see if it doesn't look curved in that area. That is why I'm thinking a cap issue.

 

It does look a bit curved. It's a duralast cap/rotor kit from autozone with 5 yr warranty. I've already swapped it out with another since it's under warranty and it sealed same way. Think any water could get in there or should I stop worrying?

 

Is it making contact with the gasket? It is no big deal IMHO. If you don't drive through river & stuff you should be OK. As a rule AutoZone has good parts. I haven't had any trouble with theirs stuff. Have you thought of driving it over to the store you bought it from & asked one of the guys to take a look at it.
I wouldn't loose any sleep over it. At worse case you could always do as we did off-road racing & seal it with a little silicone around the cap & distributor. When you first described the gap I thought it was an 1/8 of an inch or so.

 

Yeah I've asked employees there and they think it's fine as long as the gasket's in there. Which silicone you talking about?