I wanted to get a Kintetsu Limited Express from Osaka to Toba. The website says that I need to purchase a regular train ticket separately from the Limited Express. Is that correct? How do you do this online?

https://www.kintetsu.co.jp/foreign/e...ss/ticket.html

Correct, it does say that. It also says that you need to buy the basic fare ticket at the station or travel agency, etc. I started to buy a ticket, but it won't work until 5AM JT. I would expect to be only able to buy the limited express (l'ex) ticket online. Buying the basic fare ticket at the station using a machine is a bit of a hassle but those tickets are not limited, not linked to a specific train. IOW, they are not going to run out of basic fare tickets for your l'ex train.

Before boarding a train | How to get on a train | Kintetsu Railway Co.,Ltd.

They do have a ticket that combines the two charges into one physical ticket. Buy that at the station, I think. IDK how the digital l'ex ticket works, but if I had two physical tickets then I would put both into the gate together at the same time. Maybe you scan the l'ex ticket and then insert the fare ticket or v.v. IDK.

Looks like your base fare would be ¥2,460 but your l'ex ticket could be ¥2,580 or ¥1,640 which is odd. But that is what this fare search seems to be saying:
Kintetsu Corpoation -Route/Fare Search-

You can probably buy the base fare ticket a few days in advance, maybe a week or a month, but check on this if you don't want to buy it on the day of travel.

Buying from a travel agent is possible, it says. That could be useful if the ticket machines look too complicated. The only hard part of DIY is finding out what your base fare is. If you buy one that is not enough for your trip then the ticket gate at your destination will complain, and you have to pay up at a machine before you can exit.

The route map is useful. You will probably go to Namba and then find the Kintetsu Osaka-Namba Station/Lines
Limited Express Network | Kintetsu Limited Express Information | Kintetsu Railway Co.,Ltd.

And this is of general use in Japan:
Route Search - Japan Transit Planner | Norikae Annai

The guessing in the above is based on knowledge of JR ticket use, not Kintetsu, but I expect they are similar.