Did you remove the engine yourself? If so you probably have a decent mechanical mindset to do a rebuild. A quote of $1,000 by a shop before they have even taken the engine apart to see what is broken is a bit perplexing to me. Then again, I do all my own wrenching so maybe I'm out of touch of the cost of labor now a days. The bottom end of the klr 250 is actually quite stout, everything rides on caged ball bearings and there should be no reason to have to split the cases. I bought a used klr 250 bottom end on eBay several years ago that dropped a valve and put a hole thru the piston filling the crankcase with metal. I split the cases flushed the metal out and rebuilt it as one of my spare engines. So even with severe damage to the top end, the bottom end should be fine minus some cleaning of debris. Here's a short video clip I made when I had the spare engine cases apart. As you can see there's not much in the bottom half of the crank case. Two counter balance shafts, the crankshaft, input and output transmission shafts, along with the associated shift forks and shift drum. There's only a few special tools needed to do the rebuild, a flywheel puller, torque wrench and feeler gauges. The rest are common hand tools, wrenches and sockets. I source most of my klr 250 parts on eBay since the prices are cheaper than going OEM at a dealer and most of these parts are low mileage compared to my bike with over 75,000 miles. Heck if you lived near me I'd offer to help you rebuild yours.