Well the f250 had a 460 in it when we got it but when we pulled the motor, the motor mounts where hacked up and the bell housing was split into three pieces. So I found a 351m bellhousing and motor perches. Also I have ordered motor mounts from west coast broncos.

Now my question is what flywheel do I need? Not sure what year engine I have. And am not seeing a part number on the old one.

What questions do you need answered to answer my question?

 

If the 460 is externally balanced (79 & up) you need a 460 flywheel from the same years. If its an internally balanced engine you will need a zero balance flywheel. A 460 never came with a stick when they were internally balanced but a flywheel from a 390/360 will work, thats what I have in my truck. To tell weather you have internal or external balance look for a large counter weight behind the balancer, if you have it then its externally balanced. If you just have a sleeve behind the balancer than you have an internally balanced engine. I'm sure theres lots more ways but this is what works for me. You could also see if your current flywheel is weighted or weight removed in anyway.

Edit. Here's the weight and sleeve I am referring to.

 

I don't have one of the weights on it. Should I just get a 360/390 flywheel?

 

I went through all of that with my truck and my advice is just buy the summit pn FMS-M-6375-Z460B for $280 then get a new 12" long style clutch and everything else bolts up with all the stock parts. You can save yourself a lot of headaches from trying to cobble it all up. People on here have talked about having starter problems, pilot bearing problems, bellhousing spacing problems and on and on when they try to use a FE flywheel and in the end having a little 11 or 11.5" clutch in a big heavy truck that needs a 12".

 

I don't think the 390 flywheel has any effect on the problems you listed with the exception of clutch size and maybe starter problem. The issue with bell housing depth & pilot bearing is- some people say the input shaft pushes on the crank. If thats the case you could remove the flywheel all together and still have that problem.
I used a 390 flywheel and it all went together like stock. Starter sounds great. I guess I have smaller than 12" clutch but it has never slipped. It's a half ton on 33's, I could see the 12" clutch being real important if I had 42s! I have ported C9 heads, compression, cam, carb, intake, headers etc so it runs decent enough to twist the pinion off the 9" and break the drive shaft yoke. Its no aluminum head stroker that a lot of guys run but it runs good.
I'm definitely not knocking your flywheel, its clearly better. If money were no object I'm sure everyone would run it. If I ever have my engine or trans out of my truck I might actually buy the flywheel you suggest and save my FE flywheel for another 460 swap of lesser power, I think the 79 in my sig could use such an engine. I would only swap my flywheel out for the peace of mind of a larger cutch if I would ever hook to a sled or something along those lines.
I would let your budget make the call. If you have the money then go with Mark's flywheel. But if you want something cheaper, and in my experience works flawlessly then here's one for $89. Northern Auto Parts: - Valeo Flywheel V2101S by VALEO SERVICE U.S.A.