(1) No .... u cannot institute a complaint after lapse of 45 days
(2) yes ... u need to redopsit the cheque again to the Bank to go for legal action
(3) First U should redeposit the cheques ....... then after it's dishonour by the Bank u should give legal notice within 30 days from the date of it's dishonour to the Payee .... where u state the facts and demand the cheque amount within 15 days from the date of receipt of the notice by them ( send the notices by Regd. A/D only ... so that u get acknowledgement .... do not send by courier )
After the lapse of the 15 days from the date of receipt of notice by them if they do not pay then it is an offence u/s - 138 of the Negotiable Instruments Act.
U can institute a complaint with the M.M. court within one month from the date of the offence ( i.e., end of the 15 days notice period )