At startup, car runs rough. After short time it clears up and runs ok. I put in Seafoam to remove possible moisture in gas.

Seafoam is for removing carbon deposits on 2 Stroke engines.
Fuel pumps either work or they don't. They don't 'almost work' and cause an engine to run rough.

You are subscribing to the 'let's try replacing this' method of car repair. It doesn't work and is expensive. You can't guess that maybe the O2 sensors are faulty. You diagnose the DTC trouble codes using a scan tool. That will tell you the state of sensors. If you want the WHOLE story, you buy a $3.5k scan tool computer or call a mobile auto electrician.

Things you can try for free. Clean the Throttle Body and MAF, clean the IAC (idle air control).

I'd get your injectors rebuilt, and tune up your injector pump. Run a little seafoam in the diesel tank, and in the oil. Should make it clear right up.

Very easy! Get a siphon and get all of the fuel out through the fill hole. Then put 5-10 gallons of good fuel with a can of Seafoam this will help to dilute any remaining diesel that is left. Start and let idle for at least 10 minutes. It may run rough for a little bit but will clear up and you will be ok! Good Luck!

Any vacuum leaks? Timing good? egr and o2 sensors good?

valve seals are going. when car sits excess oil gets past the valve seals then when you staRT up it burns the oil off then runs fine and no more blue smoke. It is fine to run like that had the same in a dodge caravan 1996 6cyl. ran another 100 000 km. and still ran fine got rid of it for other reasons.

a car that idles rough and clears up is the sure sign of an o2 sensor shorted this may not give a code if the short in the sensor is bad the computer will eliminate its input to protect itself

try cleaning ur intake with throttle boby cleaner, an run some injecter cleaner through ur gas tank or use seafoam... (great stuff is seafoam).
if prob. persist check for vac. leak (u can replace all vac hoses for around $20-$25 bucks)
these 2 things should clear it up and r good things to do anyways weather it acually fixes it or not.
if thos dont work check ur sensors (tps, ias) u can go get a free check engine serv. done at autozone then ref. the codes to figure it out or let me know.
good luck and good jeepin

very likely the fuel injectors are damaged, replace them, the fuel pressure regulator and all rubber fuel lines, also pull the gas tank and replace the short rubber hose at the electric fuel pump, I know this is expensive but even a few miles of running would have wrecked havoc on the rubber components, that rubber debris will flow through the fuel system and will plug the injector's, E85 melts it and skin for that matter.

Do a three-part Seafoam treatment to see if it helps. You can buy Seafoam at a parts store or in the auto section of walmart. Get two cans.

Pour one entire can into the gas tank. This will clean the tank, lines, filter, injector pintles, etc.

With the other can, pour half into the oil, drive 60 miles or so, and change the oil and filter. This will remove oil sludge, varnishes, and deposits.

Remove the vacuum line from the vacuum pump on the back of the engine (or any other vacuum line into the engine), start the car, and with someone holding about 2000 RPM on the engine, allow the engine to **** up the last half can of Seafoam. It will stumble and run rough. Let it run for about 10 seconds after the Seafoam is sucked up. Then shut it down for 10-15 minutes so the Seafoam can go to work breaking down the carbon deposits in the engine's vacuum system. Then restart the car, let it idle for a couple minutes, then rev it several times to 4-5000 RPM. You should be seeing a LOT of smoke out the back of the car. Let it idle again and rev it up every couple minutes. Do this until you're not seeing much or any smoke. A little bit the next time you drive is fine - it'll finish burning off.

I've done this on many cars (most of them Audis) and it's made nice differences in smoothness, economy, and a little power even.

Also, make sure your other fluids are topped off, your air filter is clear and clean, the tires are inflated properly, and that you have no stored codes in the computer (stop at AutoZone and ask them to scan the ECU for codes - some latent codes won't trip a check-engine light but can alter the car's performance).