am i going to damage my engine.

recently got my bike and removed the ais, exup, took the cat out of the exhaust and the exup bits out of the pipe and welded it back together (hell of a job and wouldnt do it again) and cut of the flapper. primarily was to just clean up the bike and make maintenance that bit easier to do. Now i am worried because i have not got a programmer fitted and am probably running very lean.
am i going to potentially ruin my engine.

To date I've not heard of anyone ending up with a "ruined" engine from the mods you've described.

The battle cry from the dawn of time has been that these bikes come from Yamaha running a touch lean, and that mods to intake and exhaust which free up the movement of air tends to lean the bike out even more.

More air, same amount of fuel = leaner conditions.

Getting a fuel programmer will help in many ways, including just the overall smoothness of power delivery and throttle control.

The majority of people who get a programmer are happy with the changes it makes in how the bike responds.

Will you kill your engine without a programmer? Can't say yes or no for sure.
Would you enjoy life more with a programmer? Based on everything I've been reading for years, and my own experience, yes.

You got pictures of all the stuff you gutted from stock exhaust? Post them please. Post pictures of your modded exhaust all welded back up and stuff too.

On my bike, I ran an auto tune as I modified it. IMHO Yamaha had the fuel curve more than rich enough to protect the engine with air box & exhaust mods. The most common complaint with mods & no tuner is a lean stumble just off idle which is lean from the factory for emissions compliance. You can tune around that with the throttle position sensor.

funny you should say it is running rich stock. i always had problems starting with the stock engine, then as soon as i cut the flapper door off it started first time.

related to the original post but perhaps the wrong section is that i seem to have an 02 sensor positioned to the right rear of the battery going into the air intake. would this be a problem with a fmf programmer and if so, should i choose the power commander five programmer because it has an o2 sensor.

i think i read somewhere that with the fmf programmer, the o2 sensor will correct the adjustments made to it. unfortunately, i truly live far away from civilization or specifically (somebody with an dyno), so i would not beable to program around this.

so bottom line is what should i do. should i cut the o2 sensor off (no plug), or buy a more complex programmer, either of which i dont really want to do.

any advice would be greatly appreciated!

i can post pictures of the stuff i removed. one thing to note, is when i removed the cat and welded it up together the pipe came in about 5mm short, so it didnt fit in the previous position and had to be further modified

If yours came with  the O2 stock, I would leave it alone unless you have a problem? Typically any issues from pipes or airbox mods are just at or near idle. Generally you can tweeking the TPS or CO setting to fix that.
I have not work on one with the factory O2

So u wouldn't try and boost the performance at all. Feeling a little disappointed with that. A bit more responsiveness and power would have been a nice treat.

I didn't mean don't modify the bike, I meant I wouldn't disable the O2 unless you have issues you can't tune out with it functional. IMHO the factory tuning is not that far off for bolt on mods.

YMMV

That's not an O2 sensor just behind the battery, it is a temperature sensor for the air going into the engine !

thanks for that vital bit of info, should have checked the manual. if i had a sensor where would i find it? thats kind of a double edged sword, i feel compelled to by a fuel programmer now.