Help can't do squats and deads!

are you good to go? that is, did you ask your physician's advise if you're able to lift?

may i know how old you are? if yes, please state your age.

mr. dashin,

but your physician says you're okay to do other exercises?

if you're having problems with your knees, then it's best to ask a physician, because they're the experts.

in any case - if you're looking for a workout w/o those lifts, then you should check scooby's workouts in his webpage, because scooby doesn't include those in his workouts.

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Please get that checked up by a physician.  

www.scoobysworkshop.com/index.htm

Seated press, bench press, incline bench, chest supported rows on a bench or table, chinups/pullups, pullovers etc. Maybe neck bridges from the hips with some weight on your stomach, I don't know.

MercNil, physicians are NOT experts. I had trouble with my knees for a long time and nothing doctors told me or prescribed me helped. I had to figure out what was wrong by myself through almost two years of trial and error. Quit spreading this shit. I can honestly say that I trust random internet forums and my own gut feelings more than so-called "experts" after having had bursitis seven or eight times as well as unexplained knee pain every day for about a year. OP is doing the right thing.

If your knees are as bad as you say, leave them out altogether, theres a case for "they'll get used to it" but if yours have gotten worse just from general overuse just leave them be. Glute ham raises could be a option, but the purpose of this next couple weeks was to give them a break, so Imo, do just that!

And yes! The whole point of the extra sets is so that you can still grow below the hypertophy rep range; http://www.askscooby.com/advanced-bulking-up-and-gaining-muscle/growing-below-hypertrophy-rep-range/
Read that, it's a great article.

Keep it heavy! I do sets of 5 generally, if joints don't feel great maybe 4x8 of a 10rep weight, to still train but to chill out slightly (rarely happens.)

Paralysis-
Very helpful Thanks!

I say take some time off all together. Stop lifting, stop running, stop everything. Keep a daily stretching routine just to stay flexible, but take a couple weeks off from activity and let your body recover. Watch movies, surf the web, read, etc. The basic formula for treating most knee injuries is RICE - Rest, Ice, Compression, and Elevation. But any doctor will tell you the most important component of that treatment is rest.

If two weeks from now you have no pain, go back to whichever activity is most important to you, but only that activity. Take it easy and see how your body responds for a couple of weeks before you take it any further. You can't reasonably expect your knees to hold up squatting, running, and playing sports on a weekly basis. Each of those on their own can fatigue your joints depending on how hard you are pushing it. Doing all three together is going to take its toll.