First of all, Welcome to AFM.
With 110K miles on the clock, I would also consider replacing the clutch. There are alot of choices out there that won't break the bank. King Cobra for instance is a decent clutch for little coin. Spec Racing also makes a damn fine clutch and are very reasonable. My personal choice would be a Spec. With your listed mods and the fact that you are planning more in the future, I would suggest a Spec stage 1 or stage 2. Their Stage 1 in 10.5" is rated at 480ft/lbs which is more than enough for most guys unless they are going with a turbo or super charger. Their stage 2 is rated at 550-560ft/lbs for those applications. The stage 1 goes for $209 for a 10.5" or $229 for an 11" and the stage 2 sells for $319 for the 10.5" and $339 for the 11". Most 4.6 motors in stangs use a 164 tooth flywheel which calls for the 11" clutch.
Don't buy another flywheel until you've torn down the clutch etc... to get to the flywheel so you can see what kind of shape it is in. In most cases, the flywheel can be "turned" like a brake rotor and cleaned up and re-used. While you're in there, it is also a good idea to replace both the pilot bearing in the crank and the rear main seal in the back of the engine, especially with that kind of mileage on them.
I know you said you were going to take it to a dealer to have the work done but that'll cost you easily $400+ labor alone. It really isn't hard to change these out and I/we can walk you thru the entire process if you are interested. All you really need is a good set of basic hand tools both standard and metric. Of course, air tools make the job alot easier but hand tools will do it just fine. You'll also need a good jack and a set of jack stands. The only "specialty" tool you'll need would be a torque wrench but other than that, it really isn't that hard. Plus it'll save you alot of money and you'll have the satisfaction of doing it yourself. :hihi:
Good luck and let us know if you have any questions.
Tremec TKO, T45 & T56 Transmission Systems
Resident manual transmission/driveline guru :hihi:
Tech Sales Support
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TKO, T45, 3650, T5 & T56 Transmission Systems
2199 Summerfield Rd
Cookeville, TN 38506 (931) 646-4836