Can a bad alternator cause a MANUAL transmission/clutch to fail or vice versa?

A few days ago I started having trouble shifting into gear with my 5spd manual 2000 Ford Ranger. I suspected it might need a transmission fluid flush, so I went underneath and changed it.

When I went to start it up, the alternator was dead (I had it checked at Auto Zone).

Is it possible that either A) I messed something up underneath, as with a manual you don't go under the hood to change transmission fluid or B) perhaps the alternator was already going bad and caused the transmission, or possibly clutch, to fail?

All I know is, when it rains it pours!

There are a couple of reasons as to why shifting into gear can be difficult, clutch and pressure plate issues quickly come to mind or synchronizers in the trans but the alternator is part of your truck's charging system and in no way affects shifting.

No… Not a chance.

The transmission and alternator don't affect each other. You're just having a string of bad luck with your truck. It's just like you said: when it rains, it pours.

No your alternator was probably already bad.

It's uneducated people like you who keep us mechanics in business. Thanks!

Note that a manual transmission can't be "flushed" - unless you mean that you simply drained and refilled it twice? Whatever. NO, the alternator has NOTHING to do with the "clutch or transmission", LOL!