I considered MTM loss to be a negative value.
So shortfall = SPAN increase - (-ve MTM) = SPAN increase + MTM loss
case 3: if SPAN margin is increased by 5000 and there is no MTM loss/profit, then they will give you sufficient time till EOD to add funds. but if RMS team thinks your positions are at high risk and if they expect high volatility ahead, broker may square off all your positions at their own discretion, if you do not add funds after margin call. exchange has nothing to do with this, since it is the responsibility of broker to collect margin while entering positions and margin files are updated by broker to exchange only at EOD.
if at EOD you have margin shortfall, exchange will block margins from brokers working capital and broker will charge interest on their money that is blocked by exchange on behalf of your positions.
case 4: depends on magnitude of MTM loss. if SPAN margin collected while entering is enough to cover your MTM loss, there won’t be margin call. if your MTM loss crosses that threshold, broker will ask you add funds to avoid square off.