As other mentions, your major problem is the transit within Tokyo, not the one to Tsukuba because you are traveling in opposite direction of anybody else.

Just a brain storming : When I flew Haneda and enter Tokyo with Keikyu, most people got off at Shinagawa station. It probably feasible to do

Shinagawa => Asakusa (Toei) >> Walk >> Asakusa (TX) => Tsukuba

just to avoid JR.

In addition for just Yamanote line, you should check if it is feasible (aka space avaliable) to do Keihin-Tōhoku line instead. In theory shinagawa is the first major station in Tokyo and train should start free-ing up (as people change train to Yamanote line)

Or, if its easier, book an hotel in Ueon / Akihabara area instead