if it's offseason and rosters ar ejust a mess because of timing, you can also go to that team's 'roster and transaction' screen and select 'have AI setup complete organization" from 'available actions' drop-down.
if it's a league-wide problem, filling by level is best or ghost players are way easier options.
1 - can't improve stamina. you cna hurt it by overworking a pitcher. that's most likely relative to time period of historical play? anyway, not destroying them in their early years is actually beneficial in ootp.
2- will be fixed by an autocalc of league total modifiers before season starts. no, i don't think 85 home runs is accurate for that year
yes, it will happen if you don't change something before the season starts. maybe it's not 85, but an environment that can produce such an outcome is clearly not good for your context.
4. do you have minor leagues at that time? reserve clause? rhetorical questions that will help you answer why.
also, before FA, you own the players. they only leave if you release them. they will auto-renew until FA rules are enforced or you turn them on etc.