First you'd have to find a way to convert your format to a datetime. The subquery below does that by making it look like an ODBC canonical date and then calling convert. Then you can combine more convert with datediff to get your desired output format.
select convert(varchar, startrun, 105) + ' ' +
substring(convert(varchar, startrun, 109), 13, 8) + ' ' +
substring(convert(varchar, startrun, 109), 25, 2)
, convert(varchar, endrun, 105) + ' ' +
substring(convert(varchar, endrun, 109), 13, 8) + ' ' +
substring(convert(varchar, endrun, 109), 25, 2)
, substring('0' + cast(datediff(hh, startrun, endrun)
as varchar), 1, 2) + ':' +
substring('0' + cast(datediff(mi, startrun, endrun) % 60
as varchar), 1, 2) + ':' +
substring('0' + cast(datediff(s, startrun, endrun) % 60*60
as varchar), 1, 2)
from (
select convert(datetime,
substring(startrun,1,4) + '-' +
substring(startrun,5,2) + '-' +
substring(startrun,7,2) + ' ' +
substring(startrun,9,2) + ':' +
substring(startrun,11,2) + ':' +
substring(startrun,13,2),
120) as startrun
, convert(datetime,
substring(endrun,1,4) + '-' +
substring(endrun,5,2) + '-' +
substring(endrun,7,2) + ' ' +
substring(endrun,9,2) + ':' +
substring(endrun,11,2) + ':' +
substring(endrun,13,2),
120) as endrun
from @YourTable
) as SubQueryAlias
Here's a working example at SE Data. See this question for exporting the result of a query to a CSV file.