Cost to replace starter & flywheel on a 2003

rear main seals replacement is a big job as the transmission , flywheel /flex plate has to be removed
allow a minimum of 4 hrs and up to 8 hours labor for the job
get quotes from accredited service centers

you will need a replica flywheel and new bolts plus torque range and manfacturers specs.

Trans Repair Shops quote a price to pull it
& then once apart & they know the extent of
the damage,quote you a repair cost

As per Motor Professional Edition Labor Guide the allotted time is 7.4 hours.

You would need to provide more information for an exact estimate such as auto or manual trans, trans model and engine size. I'll assume it's the most popular 4.0L with an auto trans and 4x4. The book time to remove the transmission (depends on which labor book) is 5.8 hours plus .3 flywheel removal plus approx .5 to replace the plugs. The cooling system will have to be purged of air .8 and the coolant should be replaced. Multiply 7.4 hours times the shop rate example: $99.00 per hour would be approx. $740.00 in labor plus parts. Freeze plugs are cheap and coolant will be approx. $25. Good luck :o)

For a basic "tune-up," the rates as low as $30-$50 in places where the cost of living is low, to as much as $100 or more in expensive areas where more is included in the tune-up.
Most places will charge you for parts and labor separately. Often tune-up parts like spark plugs, air filters and fuel filters will run $20-$60. The hourly labor quotes are from $40 an hour, to over $110-$150 an hour at BMW and Mercedes dealerships in urban areas. In the San Francisco Bay Area, the ordinary repair shops charge rates from $55-$80 an hour, and ordinary dealerships rates of $80-$90.
Dealer 30k, 60k or 90k mile tune-ups can run from $250 for 3-4 hours of labor and basic maintenance, to over $1,000 at places with high labor costs and additional maintenance services, such as timing belt replacement.
If the mechanic identifies needed repairs, this can add a significant amount to your total.

This can be accessed by removing transmission and flywheel. Just call a dealer or repair shop for a quote. Should be about 5 to 6 hours labor and 100.00 parts.

$400.00 to R&R Trans,e.g. remove and reinstall.
6 Hours
$1800.00 to rebuild
$2200.00 total

Yes the transmission has to come out to replace the flywheel. An depending on how nice the shop will be to you, the labor hours can be 4 to 6 billable hours plus parts. What ever the going shop rate is where you live. 90$ + per hour. It mre than likely has damaged teeth on the ring gear. The factory had a spacer/shim around the nose of the starter. Did you have to deal with that when you replaced the starter> They very often don't get reinstalled and are a bit of a pain to get into place properly. Without the shim the spacing would not be proper and possibly cause premature wear to starter and or Ring Gear.