I admire your gusto! I think it's doable, and you can definitely pull it off if you want to. To replace MD5 and implement signatures you need to do the following, as a high level overview:

Extend dpkg to know what SHA2 is, and reliably detect it. (maybe measure hash length or specifying a new version using the control file?)

dpkg must also know what a signature is. More on that below.

Providing automatic/mandatory signing will require code to handle PKI as well as a place to store the signing information. I would do it by signing the two archives found within Deb packages, then placing information about the signing in the top-level of the package. Existing tools need to be able to ignore or handle whatever you implement as a rule of thumb.

Note that this is just my approach and maybe you can do better.

I also recommended looking into https://lists.debian.org/debian-dpkg/2001/03/msg00024.html. This is the thread I mentioned earlier, in which package signatures were discussed and ultimately turned down. Maybe the easiest approach is to re-implement what the contributor was trying to do back then, but with modern code and standards? If you want more resources, including my presentation on the topic to HackCFL and CitrusSec, let me know. I am here for whatever technical assistance or industry contacts I can provide. The white paper might be done in a month, minus peer review. I'm very busy and so is he. Good luck in any case!