If I recall correctly, there are new rules which state that QF will not check your bags through to your final destination if your onward flight is on MH. They will only check them in onto SYD.
If the QF CBR/SYD/CBR flights are booked in the same pnr as the MH flights then QF in CBR can through check your bags CBR/FCO. If separate pnrs, QF will only through check bags to other OW carriers which doesn't include MH.
It would be worth calling MH to ask if they "common-rate" CBR with the SYD fare, or even if there's a nominal surcharge to have CBR included in the cost of the international ticket & if so they can add the QF flights into the MH pnr.
Keep in mind that if QF only tag your bags to SYD you can't take your suitcases on the QF shuttle bus to the international terminal so you would need to collect your bags at T3 then buy a ticket on the train around to T1 international, however if bags are through checked to FCO you can take the QF shuttle bus airside which is free.
DJ might be a different story (i.e. I think they might allow through-check).
Check with DJ at CBR Airport rather than ringing res & ask if DJ through check to MH & if so do flights have to be booked in the same pnr or is it ok for 2 separate ones. I would also ask the same question of ZL.
If you can through-check your bags, then a connection time of 90 minutes will be comfortable.
If not, I'd allow 2-3 hours, preferably 2.5-3 hours just to be sure. This allows some breathing space to collect your bags, make your way to the International terminal (T1) and have some buffer for delays.
Ditto with the 3 hours. If your MH flight leaves SYD at 1540 I would want to arrive in SYD around 1240 thus allowing half an hour to disembark & collect bags & half an hour to get from T3 to T1 by train in case you just miss one. This should leave you with a comfortable 2 hours to check in at SIT with MH.
Check with MH but as far as I can tell check-in (bag drop) closes 60 minutes prior to departure. This is a fairly standard time limit across most carriers. MH probably says you
should check-in at least 2 hours beforehand - this is enough time for people to easily check-in and pass through security with minimum fuss. It's also used as a tactic to ensure they don't get people rushing for check-in when it's about to close

. But the bare minimum and book closing time is usually 1 hour before departure.
Make sure you ask MH if you can allocation your seats now for all your flights & ask if they need your passport details for immigration purposes which will streamline the checkin process. Do MH offer OLCI?