Q1: Yes. You ask ``If $X$ is a countable dimensional dense subspace of the Banach space $Y$, are the operators on $Y$ which leave $X$ invariant dense in the operators on $Y$?" Use Mackey's argument for producing quasi-complements (just a biorthogonalization procedure, going back and forth between a space and its dual) to construct a fundamental and total biorthogonal sequence $(x_n,x_n^*)$ for $Y$ with the $x_n$ in $X$; even a Hamel basis for $X$. Now use the principle of small perturbations to perturb an operator on $Y$ to a nearby one that maps each $x_n$ back into $X$. I am traveling now and so can't provide details or references, but I think that is enough for you, Yemon. The key point is that the biorthogonality makes the perturbation work--if $x_n$ were only a Hamel basis for $X$ it is hard to keep control.
I have my doubts whether this result appears in print even if oldtimers like me know the result as soon as the question is asked.
EDIT 7/4/10: Once you get the biorthogonal sequence $(x_n,x_n^*)$ with $x_n$ a Hamel basis for $X$, you finish as follows: WLOG $\|T\|=1$ and normalize the BO sequence s.t. $\|x_n^*\|=1$. Define the operator $S$ on $X$, the linear span of $x_n$, by $Sx_n=y_n$, where $y_n$ is any vector in $X$ s.t. $\|y_n-Tx_n\| < (2^{n}\|x_n\|)^{-1}\epsilon$. On $X$ you have the inequality $\|T-S\|<\epsilon$, so you get an extension of $S$ to $Y$ that satisfies the same estimate on $Y$. In checking the estimate you use the inequality $\|x\| \ge \sup_n |x_n^*(x)|$; i.e., biorthogonality is crucial.
To get the biorthogonal sequence, you take any Hamel basis $w_n$ for $X$ and construct the biorthogonal sequence by recursion so that for all $n$, span $(w_k)_{k=1}^n = $ span $(x_k)_{k=1}^n$. At step $n$ you choose any $x_n$ in span $(w_k)_{k=1}^n $ intersected with the intersection of the kernels of $x_k^*$, $1\le k < n$, and use Hahn-Banach to get $x_n^*$.
The Mackey argument I mentioned gives more. If you have any sequence $w_n$ with dense span in $Y$ and any $w_n^*$ total in $Y^*$, with a back and forth biorthogonalization argument you can build a biorthogonal sequence $(x_n,x_n^*)$ s.t. for all $n$, span $(x_k)_{k=1}^{2n}$ contains span $(w_k)_{k=1}^n $ and span $(x_k^*)_{k=1}^{2n}$ contains span $(w_k^*)_{k=1}^n $. This is quite useful when dealing with spaces that fail the approximation property; see e.g. volume one of Lindenstrauss-Tzafriri and, for something recent, my papers with Bentuo Zheng, which you can download from my home page.
EDIT 7/11/10: Getting a general positive answer to Q2 would be very difficult. Although not known to exist, it is widely believed that there is a Banach space with unconditional basis upon which every bounded linear operator is the sum of a scalar multiple of the identitydiagonal operator and a compact operator. On such a space, the operators that map $\ell_1$ into itself would be dense in the space of all bounded linear operators.