What is the Cold Cranking Amps rating on your batteries? Are your twin batteries setup in parallel or with some split charging arrangement?
Your alternator will be able to charge a bigger battery with no problem but like MRMP says it may make no difference. It's all about the cranking current capability. I wouldn't move the batteries either. You'll have to use massive cable so as to avoid volt drop over the extra distance from the starter.
There are expensive options to deal with cold starting problems such as using a diesel heater to pre-heat your engine. It'd start from warm every time and cut right back on engine ware but cost 1000's

Not really an option. Back in the day when cars were cars some manufacturers used to offer a mains powered emmersion heater as an option

I bet they did the trick on cold mornings!
Anyway my money is on the current capability of your battery. Mine is 680A and I have had (touch wood) no problems.
Steve