So, I've owned my 99 TJ 4.0L for about 10 months now and it's starting to have serious problems starting.
I'll try and start it in the morning and it'll just crank and crank and crank. The engine sounds like it's flooded; after usually 5-10 minutes of trying it'll eventually start. The problem initially only happened on Monday morning (after letting it sit all weekend), but now it's happening almost every morning.
Whenever I left it with the mechanic it would always start fine. I even left it over the weekend and it started fine for him on Monday.
At first we thought it might be the fuel pump, so we replaced the entire assembly... That didn't fix it. Then we thought it might be the fuel injectors; he checked the resistance and they all came back okay. He unfortunately doesn't have the equipment to flow test them, so he suggested I dump a can of seafoam in and see if that helps. I dumped a can into the brake vacuum line and while it appears to be running a little more smoothly, it still has problems starting. When it finally does start, there's no plume of black smoke or stench of gas. The oil smells clean of gas as well.
This morning my neighbour suggested it could be a relay; seeing as all the relays in mine are the same, I figured I'd try shifting all of them one position.
It's only thrown one code, once. After a really hard start my CEL came on. Thankfully a guy at my work had an OBD reader; it came up with P0301, Cylinder 1 misfire. However, once I started it about an hour later the CEL was off. It hasn't reappeared since.
At this point I'm at a complete loss. The battery is 6 months old, the oil & filter were changed in June. I bought a new distributor cap (still need to install) and another can of seafoam-- but I'm just blindly throwing money at it in the hopes something fixes it. It drives reliably and gives no indication that anything is wrong once it's running.
Any suggestions would be greatly appreciated!