1997 Silverado 1500 with starter problems

I have a 97 Silverado with just over 200,000 miles. I recently replaced the entire motor with a turn key crate 350. Since the replacement, I have gone through 3 batteries. When they're tested they are completely dead in all cells. I am also on my third starter and it's already making a clunking, grinding noise when I try to turn my truck on. I have a new flex plate and my motor was scoped. All new top end and seals. I've had mechanics try to shim my starter in every direction but it hasn't changed anything. Now they are telling me to file my starter housing, which doesn't sound right to me. I do generally work on my own vehicles but this one just keeps going. Any ideas to help?
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