2000 MR2 Spyder. Son let the engine run low on oil now it knocks really hard and wont go faster than 30 mph. Help me

the sound may be the hydraulic lifters need to fill with oil before they run silent
possible el cheapo oil filter without a flow back valve used ,
oil viscosity wrong for used engine
take it to an accredited service center and leave over night so that the problem can be diagnosed on first start up on a cold engine

Try checking your O2 sensors if you have one that isnot working all the time you will get that reading. If you don't have a computer readout machine take it to an auto zone or another auto parts place they will run the diagnostic tool on your car and tell you what it is as it will give you a code

when an engine overheats that bad , the cost to rebuild is generally close to a fully reconditioned exchange engine
check the wreckers / junk yards for a good engine of the same family group as is on the compliance plate /build plate on your car ( many such places import engines with low miles/klm that are in top condition
the rebuild will include new head or head rework , new pistons and rings , bearings , engine re-bore and all of that will not include the labour charges
burning a motor is not an inexpensive experience and that is why I suggest a second hand motor or a service exchange motor for an accredited engine reconditioning shop

It seems a bad idea , Just doing a good repair is like new :

replace head valves seals
replace head gasket , also check head plain
check cylinders for wear
repalce piston rings

check oil level first then if more than qt low bring up to full level them check oil pressure on gauge as cranking car or oil light make sure these things are operating correctly if not this is problem no oil pressure then computer delays starting is this white smoke or black smoke or blue smoke?

It's really not that hard of a job as long as you have the proper tools. I would say at least a metric socket set with an extension. Probably a screwdriver will be needed too. Take your time and keep a mental note of where all the clamps were installed so when you install the new one it os clamped down and secure just like the factory intended. A loose wire could chafe and cause a short. You do not want this.

have you check the speed sensors? the check light wont be light if the sensor run off calibrate. try to visuallise the sensor if there is crack or something.

Replace the entire section before and after the flex. Be sure to look into excessive engine movement, that may have caused this failure. Welds will fail again, quickly.

use only OEM Toyota trans fluid. If there is one lesson I learned with my MR2, its that Toyotas own trans fluid is the best. Yes, its a few dollars more, use it anyway.

As for your top, there is a product called Amazing Roll off. Its for boat canvases and its simply the best thing i've ever used. try it, you wont be disappointed.

I got mine from a company called www.electronicmanuals. i think, you can buy it as a download or on a C.D.