Linda Jo, I think I confused you when I said custom-designed. I did not customize them for each person like you are thinking. I just mean that I did not buy invitations online or from a store or any other kind of pre-made template. I composed the image, designed it all myself, and had the invitations custom-made. So all my thank you's are the same and it's just the message that will be personalized. I think it would be WAY too much work to customize it for everyone (in my opinion). Perhaps you could have the same card for everyone, and of course write a unique message, and insert a customized wedding photo for your VIPs? I put a copy of the same picture in each of mine, but to make it more personal you could send your grandma a picture of you dancing with her, and send your mom a picture of you two getting ready together, etc. And then for the people you don't know as well, you could have a "standard" that you put in everyone else's. That wouldn't be quite as time consuming and would add a nice personal touch. Something to think about. I'm not sure how many people you need to send them to, but honestly I don't think most of them would truly appreciate the work you put into customizing each one and would probably be equally happy with getting the same one as everyone else. So if you really want to go that route, I would seriously consider only picking an elite group to do that for -- such as the in-laws, your family, and the wedding party (for example) -- rather than everyone. Like that person your DH hardly knows from work but got invited out of obligation... does he really need that much thought put into his thank you? Probably not. He's happy to get a note and that's all you need.
As far as the checks, it really depends on each giver. Most people probably won't think it's a big deal and will be happy just to receive a thank you. There might be one or two that thinks it's rude but they'll get over it. Always better late than never. Since you've already deposited them, I would definitely send those people's thank you's out as soon as possible and make them first priority.
Aunt, you have a point and there probably are a couple people that think I'm being rude. But I'm not going to obsess about them, because clearly they aren't the people that are important to me anyways. If my mom has a couple of friends who have nothing better to do than judge me for sending their thank you note within two months of the wedding, then I will get over that and honestly I think they are the rude ones. I do think it's rude not to send a thank you at all, but within two months is more than acceptable as far as I'm concerned. In general, I've realized that guests can be very rude in many ways.