Since the motor is out take it to a machine shop for a rebuild. You'll probably only have to drop maybe $600 which is not bad. You can probably have you fairings re-painted for a couple hundred bucks.
You seem to have adequate space to work on your bike, you should be fine. I did a resto many years ago on a 80's FZR600...beautiful bike the original fairings were in top shape. I spent about $2k buying little parts here and there, new tires, brakes, chain, and of course engine overhaul. In the end well worth the money. I love late 80's to mid 90's bikes.
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94 900RR
04 BMW Z4 2.5 M Package
01 R170 AMG Sport Package
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