OK, I did it once more and found out that it installed the files in
/usr/local/lib/ instead of /user/lib/ where it used to be.

You need to set the prefix to /usr as the default with autoconf is /usr/local

./configure —prefix=/usr/local
make
sudo make install

It also did not associate the ".pd" extension with Pd anymore so I have to
open them with "Open" from the file menu or the command line.

The Linux desktop environment specific file extension stuff from Pd-extended is not yet included with Pd vanilla.

Could I simply move the pd folder to the old directory (/user/lib/) or would
that cause problems?

See above.

I'm still having lots of problems with externals that I installed via deken.
Doesn't look like I can get my old stuff running that was originally created
with Pd-Extended.

“Lots of problems” sounds like you’re still missing requird externals and/or 

--------
Dan Wilcox
@danomatika
danomatika.com
robotcowboy.com

On Dec 20, 2015, at 10:18 AM, pd-list-request@lists.iem.at wrote:

From: "Ingo" <ingo@miamiwave.com>
Subject: Re: [PD] How to update Pd 0.45.4 to 0.46.7 0n Ubuntu 14.4 (Odroid XU4)
Date: December 20, 2015 at 10:18:33 AM MST
To: "'Alexandros Drymonitis'" <adrcki@gmail.com>
Cc: pd-list@lists.iem.at