So I have a bit of trouble with my game install.

I had BG1+2 installed in a Win7 computer, and reached the end of the first chapter in BG2, But then I had to format that computer and transfer my BG2 folder to a win 10 laptop. This is where my problems began.

At first the game told I had to reinstall again, I tried following the steps I used to install BG+BG2 in my original computer again and then just paste the savefiles to the clean install, but the game crashed and never finished loading said saves, perhaps because I messed up and installed a tweak that was not present in my original savefile.

I think I used BGT instead of tutu for the original install, plus all the usual fixes in the guide like fixpack, unfinished business and the like., its been a while, I dont remember which one of the guides present here I used originally to merge the games (at the end of BG1 I had my dragon familiar in my inventory and I lost it when BG2 started, while still mentioning in the sheet that I had a dragon familiar without the penalty for losing it in combat)

The old install refused to start altogether, so I removed the new install and replaced it with the old, modified the .ini to reflect the new path to C:\program files\Games and the game started again, even the saves loaded, but for some reason the game runs slow, jittery and it glitches out to show stuff from the desktop, also my cursor gets lost because its flickering like crazy.

I should also note that the game asks me to configure the options since its my first time running it, wich is not true, it asks me this every time I open up the game.

I have no idea if this is an issue with Win10, perhaps I should just reinstall all the patches and see what happens? I seriously dont want to lose all my progress here. I just tried reinstalling the widescreen patch according to the resolution of this computer (1920x1080 instead of the old 1366x768) and its still buggy.

BGT *MUST* be installed afresh with a virgin copy of BG1 and 2. This is absolutely critical to the core of what the mod does. You must *NOT* install any mods or tweaks of any kind before installing BGT. Bottom line: you must start afresh, and do NOT install in 'Program Files' or 'Program Files (x86)'. Install to a simple folder like C:\Games\

When I tried a fresh install to slap the old savefiles in, I used the default GOG folder of C:\GOG Games\, not Program Files, Im pretty sure I did the same on the old Win7 computer before making a backup of the install and moving it to Win10.

Perhaps I should have used something simpler like C:\Games\ instead? (I actually have no idea)

You have not heard what I said. Your words:
"I had BG1+2 installed in a Win7 computer, and reached the end of the first chapter in BG2, But then I had to format that computer and transfer my BG2 folder to a win 10 laptop. This is where my problems began."

As I said, you must install from fresh. BGT absolutely requires this.

Seems like I misread your reply, I will try and do another fresh install and see what happens.

EDIT: well, the saves work now, which is weird, considering I followed the same process as the first try on a new install, but this time using the Games folder instead of the default GOG one, and GOG Games is located in C: instead of in Program files.

I must have messed up in someplace else along the process, anyways, problem solved. Thanks for the assistance.

Classic BG2 can be transferred by just copying the game directory. Provided that path to the game is the same, it will work (launch bgmain.exe, not baldur.exe)

It can, I've done that multiple times.

Not cleanly, and certainly not an exercise for beginners or people who don't know precisely what they're doing.

I'm not sure what do you mean by not cleanly, it's straight copy, and as long as path is the same, it's all good. As for beginners, well, maybe, but that can be said about anything.

[Edit: typo]
But not clean. The installer stores version numbers and patch versions in the registry. A straight copy will be missing those entries. It also will be impossible to uninstall the games with a straight copy -- they will have incorrect or no uninstall information. It's never a good idea to straight copy any game or software unless it's specifically designed as standalone, like you can run it from a pen drive or something similar.