I have one of the basic fender squier guitars from the 99 dollar starter pack, I wanted to modify it a little - I wanted to replace the pickguard and pickups with a new pickguard loaded with seymour duncan blackous HSS, the previous pickup conifg is three single coil, I dont see a problem with this transition though right?

And besides that I wanted to instal a tune o matic bridge to this (fender squier) and most likely upgrade the tuners

I'm new to guitar construction, but I am willing to learn how to solder the electrical wire and undertake the challanges and hopefully gain the future satisfaction, so I would appreicate any advice to my proposed modifications, and probally the biggest question... would it even be wise to do all these high grade modifications to such a low quality fender squier?
Sure, if you really want to do that, go for it. It's a good way to learn how to do basic electrical wiring. You'll never get a Tune-O-Matic bridge on there, though.

Replacing the pickups with Blackouts, putting on a new bridge, HSS pickguard and upgrading the tuners all together is going to cost you somewhere around $250-$400, so do you think it's worth it? Realistically, you could buy a Schecter ATX C-1 for like $500 used.
are there any other bridge replacements possible for the fender squier, the current bridge is just so dull =/
I pmuped over $700 through my Squier, I think it was worth it.

Don't bother with the bridge, just get some good saddles, and lock it down. Whatever you do, DO NOT REMOVE THE BRIDGE!!! The screw holes that hold the trem plate down are very crappy, and with mine it ruined the screw holes so now my bridge is all jacked up.

Unless you plan on drilling new holes for a two point bridge, don't bother, you'll just make it worse.

Otherwise, go wild with your mods, bet thing to learn on is a cheap guitar.
modding Squiers is fun
I agree though, a tune-o-matic will never work. you will have to block off the trem somehow if you really wanna make it a hardtail.
honestly, if the guitar plays well and feels solid then who cares if its only a Squier. People place too much value on brands and not enough on the truly important features of a guitar.