By the time you get front lowers in chrome, switches and controls in chrome, upgrade your floorboards and brake pedal and shifter pegs, shift arms and rear brake lever, chrome wheels, upgraded stereo with all the fixin's, heated seat and grips, chrome wheels, mirrors, power locks, luggage rack, security system, custom paint, glove boxes, windshield trim, rider backrest, abs brembo brakes, add highway pegs, different turn signals, bike cover, travel bags for inside your saddlebags and tour pack, liners for tour pack and saddlebags, upgraded hardward on the luggage, chrome rotors, and I'm sure that there are many things I have missed...now you still have to start to upgrade the engine. I think you can get away with an upgrade to the 110" for probably $6000 to $7000. If you go to the 113", I'm guessing that with the other things you will want to change out at the same time, look at $8000 to $10,000 on the engine.
With all of that said, you will end up with more than a SE invested by a long shot. But that isn't the big problem. Again, as was already mentioned, if you ever decide to trade or sell your bike, you still have a VIN from a standard bike. Book values are based on the stock bike and this value is used by a bank to determine what value can be loaned against a bike. The bank does not care what accessories are added to a bike in determining the value, other than the engine will get you some more money out of it, but not nearly what you have into it. The dealer is then only able to offer you a trade based on what they feel they can sell the bike for, and they have to take into account how much can be taken on a loan to buy that bike. For instance, if you have $35K into your bike and the book value is still only $17K, the dealer knows that when they go to resell the bike, the bank will only lend based on that book value. They can't sell it for $35K, or even $25K unless they would happen to get lucky to have a customer walk in that is willing to pay cash for any of the difference. The dealer makes an assumption that a buyer will be willing to put down 10%, which means your $35K bike that you trade will probably go back out the door to some lucky buyer for under $20K. I just went through this with my 07 Road King that I had about $33K into. The dealer just sold it and got about $21K out of it. I did one heck of a nice job fixing up a bike for someone else and they are getting to reap the benefits of my stupidity.
I thought many times about buying the FLHTCU and upgrading it to match the SE, but the cost would have been way too high and I would have done the same thing to myself all over again. If you want a SE, buy a SE and don't look back. With either one, you will still have to reach into your pocket for pipes, tuner, intake, etc.