Sorry that your deal went sideways, and hoping that you're able to either close on a better note or find a better car. It took me 2 years with 1 year of more serious looking to find my car and it was worth the wait.
Wheels are easy to change even though they can be expensive. There are lots of replica Corvette wheels out there, so you can go anywhere from styles in your year, different years, early Z06, later Z06, and ZR1 that are sized for the base chassis.
#Savethemanuals all the way. The manual is such a better transmission than the automatic too, as the auto is crap for performance engagement. If you're just cruising the auto is fine, but for performance the paddles aren't well designed and the shift input times are more a suggestion of shifting.
2LT or 3LT is definitely the way to go unless the base options are fine for you. The heated seats, memory seats, and HUD are all great options, and I like the adjustable bolsters to hold me in place on back roads. The heated seats in my car are some of the best I've ever used, as they get really warm, and also heat almost up to my shoulders, so if you drive on colder days it's great. I thought the HUD would be fun and a bit of a gag, but has turned out to be one of my favourite options, both for "cool" factor and also keeping a close eye on speed. When in street mode, the HUD shows radio station presets, CD tracks, and if you have the nav (which is dated but works well), distance to turns and direction arrows which is neat. In track mode it's great for paying attention to oil or coolant temp.
I think some people in Corvette land think 55,000 KMs is high, and it probably is higher than the average Corvette for the age, but whatever gets you in the door in your budget. I think most of those are the types who don't keep their cars long, don't drive their cars a lot, like to brag about low mileage, or think their cars are rare. It all depends on condition and what you plan on doing with the car. If you plan to keep the car a long time then the depreciation is less important, and if you plan to drive a lot, you'll be adding to the mileage and increasing that depreciation. I'd rather have a well maintained regular mileage car than a super low mileage garage queen that needs extra maintenance from sitting.
Dealer fees are definitely the new scam for creative account padding the bottom line. Phil Edmontson author of Lemon-Aid used to advise to not pay dealer fees, then a few years ago he couldn't negotiate away the fee, so started telling people they might not have a choice. It's like the dealers got together and said "if we just don't say no, people will have no choice."