Please help me understand this letter

So you sent a query to an agent and this is what you get. Was there a cover letter too? It sounds like there should have been a letter saying he's interested, along with this note on how to prepare the manuscript for submission. I don't know what to tell you...it really sounds like you got half the package?

Yes...the handwritten message tells me he was ACTUALLY asking for something. I really feel there is a missing letter. Oy vey...sometimes they make it so difficult. And you feel like you can't contact them to ask because you already feel like approaching them is like walking on ice. I feel for you. I also agree with your thoughts.

There are times you simply have to call and ask. Listen they're not gods, and you have a legitimate question. Just call and say what you put in your post. Courteously ask for an explanation. If he didn't want a submission, they can't come through the phone after you. If he did, this is the sensible thing to do if you're confused by the instructions or they're accidentally incomplete, and he won't mind.

Edit: And if someone minds you calling and saying: "I got some instructions on submission in the mail from your office, and I'm a bit confused." then it's an agent who you probably don't want to work with anyway.

I agree, you should call to make sure, but my instinct tells me that it's not necessarily a request--or if it is, the handwritten part is irrelevant here. After all, you didn't submit by e-mail, so why should he suspect you would? Rather, I wonder whether he hasn't gotten around to revising the sheet on which he puts his rules for submission. And if he took the trouble to hand-write the rules about no e-mail, etc., why didn't he take the trouble to say, "Sure, I'd like to see a proposal. See above."

It is peculiar. I don't want to be a downer, but this doesn't sound promising to me. Nevertheless, call, by all means--the worst that can happen is that you're told no, and you'll have had the experience of making this kind of call, which is useful.

I say make the call. I mean, it may be painful, but maybe not as painful as sitting around and wondering.
Hope you find out that he loved your query and forgot to put the coverletter in.