Your ability to rebuild the motorcycle only adds value (in my opinion) if you are planning to resell it and are considering alternate uses of your financial resources. With any used KLR (especially one with 44K) the teardown issue is always a possibility. There may be other issues as well (swingarm bushings, fork seals, etc.) that will add to the cost of returning the bike to premium condition. Checking Craigslist for my area, the used price of 2008/2009s seems to be about $4K. If you take your $1900 KLR, add $500 for engine parts, $300-500 for exhaust, $300-500 for chain/sprocket/tires, figure in seals, rear shock, and other things that may need work, it starts to add up pretty quick. There are probably new (unsold) 06/07 KLRs sitting in a dealership for about $4K also. If the '03 was the most desireable KLR I might consider it. If I wanted a project to keep busy with I might consider it. If I wanted a ride, I'd keep looking.
"My KLR belongs to God, when he wants it clean he washes it."