I'd recommend that you start by reading through the excellent FAQ thread on the 722.6xx transmission in the W210 DIY/Help stickies.
http://www.benzworld.org/forums/w210-e-class/1463460-mercedes-benz-722-6-transmission-faq.html
Here's a stripped-down, simplified summary.
The transmission in your car is a mechanical device, but it's electronically controlled. Think DBW (drive-by-wire). The TCM connects to the conductor plate (which sits atop the valve body) via a harness that slides through the pilot bushing (connector/harness adapter) in the front right of the transmission. The pilot bushing has been redesigned at least three times since your car was made because they have a tendency to leak fluid into the harness, where it runs up the wires and soaks the TCM, triggering fault codes. (The starting point, though, is to pull the TCM and see if it is wet with fluid, if not my recommendations would change a bit, so do that first.)
The scanners that read codes can clear them from the ECU (regular old OBD-II compliance), but that doesn't clear them from the TCM. So you do a bunch of work, heck, you could even replace the transmission, and the TCM will feed the codes back to the ECU and voila, you're back in limp mode. So you need a system that will talk directly to the TCU and that limits you to SDS, Snap-On, carsoft, etc. Any decent shop that works on German cars will have the proper interface.
There are a couple of DIYs on replacing the pilot bushing in the 210 forum DIY/Help stickies. But what you need to know as tips. First, you rotate a ring on the pilot bushing to release the harness connector, then you pull the harness connector STRAIGHT OUT. Do NOT try to rotate it (this applies double when you are reassembling, if you turn it you will bend one or more pins on the conductor plate, and your day just went downhill in a big hurry). Second: there is a single very small bolt in the center bottom of the pilot bushing. It threads into the conductor plate and serves only to secure the two pieces together. It is not strong enough to pull the pilot bushing into place, if you do that you will break it or strip it. You must fully seat the pilot bushing in the transmission housing, and then snug up (not much more than finger tight!!) the little bolt. I use a nut driver on it (IIRC it's a 7mm head).
Be sure to use spec fluid, MB 236.14. If you don't know when the trans was last serviced you *could* service it at this time, but I would not (since there is a possibility you'll have to replace the conductor plate and then you'd lose all the new fluid and it's not cheap).
The only special tool you will need is the transmission dipstick tool. You'll read about that in the FAQ thread.
BTW, the reason the shop said replace the TCM is twofold. One, they don't like to clean and clear, they like to replace. Less trouble and time for them, less chance of a comeback. Two, they aren't that familiar with these cars, since they didn't mention replacing the pilot bushing, which is the likely cause of the problems in the first place.
So, to sum up: check the TCM for signs of fluid incursion. If so clean it and replace the pilot bushing, set the fluid level, have the TCM cleared, and you should be good.
Do some reading, post back if you have questions.
Good luck.